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GitLab

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<h3>

Nilesh Patra 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/a93b33f441d39ebc55c7c5a4de421ba368c63be1">a93b33f4</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-04-21T13:15:04+00:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.4</pre>

</li>

</ul>

<h4>30 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">

.github/workflows/ci.yml

</a>

</li>

<li class="file-stats">

<a href="#52839267e933c02ef22d9cabbf4740ceb41b8abe">

.github/workflows/pyinstaller.yml

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<li class="file-stats">

<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">

CHANGES.rst

</a>

</li>

<li class="file-stats">

<a href="#561b88e19de321ca62c7590bbb350765fb110905">

README.rst

</a>

</li>

<li class="file-stats">

<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">

doc/guide.rst

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</li>

<li class="file-stats">

<a href="#6677207c6fa30ac9cec19ad036ae842582159ecb">

doc/installation.rst

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<li class="file-stats">

<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">

pyproject.toml

</a>

</li>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

<li class="file-stats">

<a href="#babdfe5d368a4907abadce7f9b00dfab2489185a">

src/cutadapt/__main__.py

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<li class="file-stats">

<a href="#ecaf81c67bfb6c86fbef95a99558f4bec3b0c983">

src/cutadapt/_align.pyi

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<a href="#8fb347891ec0a40b16ef2bdbe361f823e12aa016">

src/cutadapt/adapters.py

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<li class="file-stats">

<a href="#98e6d8e6e9db700c1f73b5678eae963cb214cbc9">

src/cutadapt/align.py

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<li class="file-stats">

<a href="#6ed465db6839a69141086c2acf1dc01a8b17a981">

src/cutadapt/filters.py

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<li class="file-stats">

<a href="#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae">

src/cutadapt/log.py

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<li class="file-stats">

<a href="#a44086ebe255bc0df91ea1d82811c828e6f5e324">

src/cutadapt/modifiers.py

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<li class="file-stats">

<a href="#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5">

src/cutadapt/parser.py

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<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

src/cutadapt/pipeline.py

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<a href="#0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de">

src/cutadapt/report.py

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<li class="file-stats">

<a href="#af95dfcb30a51908f338d0fd6a196b9e4c108046">

src/cutadapt/utils.py

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<li class="file-stats">

<a href="#626af34e8204774ea46e20955936146dedc828eb">

tests/conftest.py

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<li class="file-stats">

<a href="#5668d3b26dd09e6c19b959c5cc817ff64dc54cb6">

<span class="new-file">

+

tests/cut/info-rc.txt

</span>

</a>

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<li class="file-stats">

<a href="#5fc94fc2534bb535bfd7015f641462099d4972fa">

<span class="new-file">

+

tests/data/info-rc.fasta

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</a>

</li>

<li class="file-stats">

<a href="#8b386ef32463372ea7de22d96d0771a85c1ed553">

tests/test_command.py

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</li>

<li class="file-stats">

<a href="#83ff0d8e113228f36b352922cbbb938d0aa9384b">

tests/test_commandline.py

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<li class="file-stats">

<a href="#124a8b77d32c7ca9f7f1966a0cde3894ce860e05">

tests/test_main.py

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<li class="file-stats">

<a href="#aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda">

tests/test_modifiers.py

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<li class="file-stats">

<a href="#4ad7124461a591ee5c5c2e30f24380a477c3ed52">

tests/test_paired.py

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<li class="file-stats">

<a href="#9627b71ff9952493fda5865aea912319edd1cdd2">

tests/test_parser.py

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<li class="file-stats">

<a href="#570726290219a04b926b9aa2c02fe1ba4204124a">

tests/utils.py

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<li class="file-stats">

<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">

tox.ini

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</ul>

<h4>Changes:</h4>

<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>

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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">@@ -4,7 +4,7 @@ on: [push, pull_request]</td>

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<td class="old_line diff-line-num" 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">

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

</pre>

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml">  <span class="na" style="color: #008080;">lint</span><span class="pi">:</span></span>

</pre>

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

7

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<td class="new_line diff-line-num old" data-linenumber="7" 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="LC7" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>

</pre>

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

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">10</span></span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -22,7 +22,7 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml">      <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tox -e ${{ matrix.toxenv }}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">  <span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">10</span></span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>

</pre>

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

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<td class="new_line diff-line-num" 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="yaml">    <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml">      <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,6 +31,8 @@ jobs:</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml">        <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

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<td class="old_line diff-line-num" 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="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="yaml">          <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(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="LC35" class="line" lang="yaml">          <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">windows-latest</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(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="LC36" class="line" lang="yaml">    <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(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="new_line diff-line-num" 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="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="45" style="width: 35px; color: rgba(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="47" style="width: 35px; color: rgba(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">@@ -45,7 +47,7 @@ jobs:</td>

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<td class="new_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(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="LC47" class="line" lang="yaml">      <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">codecov/codecov-action@v1</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(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="LC48" class="line" lang="yaml"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="47" style="width: 35px; color: rgba(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="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml">  <span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="48" 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="new_line diff-line-num old" data-linenumber="50" 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="LC48" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">5</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml">    <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;"><span class="idiff left right">10</span></span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml">    <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC52" class="line" lang="yaml">    <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">lint</span><span class="pi">,</span> <span class="nv" style="color: #008080;">test</span><span class="pi">]</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="yaml">    <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">startsWith(github.ref, 'refs/tags')</span></span>

</pre>

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<br>

</li>

<li id="52839267e933c02ef22d9cabbf4740ceb41b8abe">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#52839267e933c02ef22d9cabbf4740ceb41b8abe"><strong>.github/workflows/pyinstaller.yml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ jobs:</td>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Python</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">        <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v1</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml">        <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>

</pre>

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

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

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">          <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.<span class="idiff left right">7</span>'</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml">          <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">3.<span class="idiff left right">9</span>'</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml">        <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml">          <span class="s" style="color: #d14;">python -m venv venv</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,9 +18,9 @@ jobs:</td>

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<td class="old_line diff-line-num" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="yaml">          <span class="s" style="color: #d14;">venv/Scripts/pip install .</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Make exe</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml">        <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" 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="new_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "from cutadapt.__main__ import main" > script.py</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" 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="new_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "sys.exit(main())" >> script.py</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="23" 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="new_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">          <span class="s" style="color: #d14;">venv/Scripts/pyinstaller -F <span class="idiff left right">-w </span>-n cutadapt script.py</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "from cutadapt.__main__ import main<span class="idiff left right">_cli</span>" > script.py</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "sys.exit(main<span class="idiff left right">_cli</span>())" >> script.py</span></span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml">          <span class="s" style="color: #d14;">venv/Scripts/pyinstaller -F -n cutadapt script.py</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run it</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="yaml">        <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/cutadapt.exe --version</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">      <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>

</pre>

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<br>

</li>

<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>

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

</pre>

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

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

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.4</span> <span class="p">(</span><span class="m" style="color: #099;">2021</span><span class="p">-</span><span class="m" style="color: #099;">03</span><span class="p">-</span><span class="m" style="color: #099;">30</span><span class="p">)</span></span>

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

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

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">481</span><span class="p">`:</span> <span class="n" style="color: #333;">An</span> <span class="n" style="color: #333;">experimental</span> <span class="n" style="color: #333;">single</span><span class="p">-</span><span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">Windows</span> <span class="n" style="color: #333;">executable</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">Cutadapt</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel">  <span class="n" style="color: #333;">is</span> <span class="p">`</span><span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">download</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">GitHub</span> <span class="s2" style="color: #d14;">"releases"</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel">  <span class="n" style="color: #333;">page</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;">releases</span><span class="p">>`</span><span class="n" style="color: #333;">_</span><span class="p">.</span></span>

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">517</span><span class="p">`:</span> <span class="n" style="color: #333;">Report</span> <span class="n" style="color: #333;">correct</span> <span class="n" style="color: #333;">sequence</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span> <span class="n" style="color: #333;">file</span> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">was</span> <span class="nb" style="color: #0086b3;">reverse</span> <span class="n" style="color: #333;">complemented</span></span>

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<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC12" 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;">517</span><span class="p">`:</span> <span class="n" style="color: #333;">Added</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">column</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">info</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">shows</span> <span class="n" style="color: #333;">whether</span> <span class="n" style="color: #333;">the</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">was</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel">  <span class="nb" style="color: #0086b3;">reverse</span><span class="p">-</span><span class="n" style="color: #333;">complemented</span> <span class="p">(</span><span class="k" style="font-weight: 600;">if</span> <span class="p">``--</span><span class="n" style="color: #333;">revcomp</span><span class="p">``</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">used</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">320</span><span class="p">`:</span> <span class="n" style="color: #333;">Fix</span> <span class="p">(</span><span class="n" style="color: #333;">again</span><span class="p">)</span> <span class="s2" style="color: #d14;">"Too many open files"</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">demultiplexing</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="mosel"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.3</span> <span class="p">(</span><span class="m" style="color: #099;">2021</span><span class="p">-</span><span class="m" style="color: #099;">03</span><span class="p">-</span><span class="m" style="color: #099;">04</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"><span class="p">-----------------</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC19" 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;">504</span><span class="p">`:</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">crash</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">Windows</span><span class="p">.</span></span>

</pre>

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

20

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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;">490</span><span class="p">`:</span> <span class="n" style="color: #333;">When</span> <span class="p">``--</span><span class="n" style="color: #333;">rename</span><span class="p">``</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">used</span> <span class="k" style="font-weight: 600;">with</span> <span class="p">``--</span><span class="n" style="color: #333;">revcomp</span><span class="p">``,</span> <span class="n" style="color: #333;">disable</span> <span class="n" style="color: #333;">adding</span> <span class="n" style="color: #333;">the</span></span>

</pre>

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

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel">  <span class="p">``</span><span class="n" style="color: #333;">rc</span><span class="p">``</span> <span class="n" style="color: #333;">suffix</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">reads</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">were</span> <span class="nb" style="color: #0086b3;">reverse</span><span class="p">-</span><span class="n" style="color: #333;">complemented</span><span class="p">.</span></span>

</pre>

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

22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"><span class="p">*</span> <span class="n" style="color: #333;">Also</span><span class="p">,</span> <span class="n" style="color: #333;">there</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">a</span> <span class="p">``{</span><span class="n" style="color: #333;">rc</span><span class="p">}`</span> <span class="n" style="color: #333;">template</span> <span class="n" style="color: #333;">variable</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">the</span> <span class="p">``--</span><span class="n" style="color: #333;">rename</span><span class="p">``</span> <span class="n" style="color: #333;">option</span><span class="p">,</span> <span class="n" style="color: #333;">which</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="mosel">  <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">replaced</span> <span class="k" style="font-weight: 600;">with</span> <span class="s2" style="color: #d14;">"rc"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="nb" style="color: #0086b3;">read</span> <span class="n" style="color: #333;">was</span> <span class="nb" style="color: #0086b3;">reverse</span><span class="p">-</span><span class="n" style="color: #333;">complemented</span> <span class="p">(</span><span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">empty</span> <span class="k" style="font-weight: 600;">string</span> <span class="k" style="font-weight: 600;">if</span> <span class="k" style="font-weight: 600;">not</span><span class="p">).</span></span>

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

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="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;">512</span><span class="p">`:</span> <span class="n" style="color: #333;">Fix</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;">128</span><span class="p">`</span> <span class="n" style="color: #333;">once</span> <span class="n" style="color: #333;">more</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">“</span><span class="n" style="color: #333;">Reads</span> <span class="n" style="color: #333;">written</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">”</span> <span class="n" style="color: #333;">figure</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">report</span></span>

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

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel">  <span class="n" style="color: #333;">incorrectly</span> <span class="n" style="color: #333;">included</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">trimmed</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">untrimmed</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">``--</span><span class="n" style="color: #333;">untrimmed</span><span class="p">-</span><span class="n" style="color: #333;">output</span><span class="p">``</span> <span class="n" style="color: #333;">was</span> <span class="n" style="color: #333;">used</span><span class="p">).</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">515</span><span class="p">`:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">report</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="nf" style="color: #900; font-weight: 600;">send</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">stderr</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">any</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">is</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel">  <span class="n" style="color: #333;">written</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">stdout</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="mosel"><span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.2</span> <span class="p">(</span><span class="m" style="color: #099;">2021</span><span class="p">-</span><span class="m" style="color: #099;">01</span><span class="p">-</span><span class="m" style="color: #099;">07</span><span class="p">)</span></span>

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

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="mosel"></span>

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</li>

<li id="561b88e19de321ca62c7590bbb350765fb110905">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>

<hr>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.. image:: https://<span class="idiff left">travis-ci.org</span>/marcelm/cutadapt<span class="idiff right">.svg?branch=master</span></span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.. image:: https://<span class="idiff left">github.com</span>/marcelm/cutadapt<span class="idiff right">/workflows/CI/badge.svg</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">    :target: https://travis-ci.org/marcelm/cutadapt</span>

</pre>

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

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

</pre>

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<li id="ee1d7278a009e2c5c652622fe43dc77e39af740d">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1099" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -1099,6 +1099,8 @@ The following placeholders are currently available for single-end reads:</td>

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<pre style="margin: 0;"> <span id="LC1099" class="line" lang="plaintext">  used with a positive length argument)</span>

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<pre style="margin: 0;"> <span id="LC1100" class="line" lang="plaintext">* ``{cut_suffix}`` -- the suffix removed by the ``--cut`` (or ``-u``) option (that is, when</span>

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<pre style="margin: 0;"> <span id="LC1101" class="line" lang="plaintext">  used with a negative length argument)</span>

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<pre style="margin: 0;">+<span id="LC1102" class="line" lang="plaintext">* ``{rc}`` -- this is replaced with the string ``rc`` if the read was reverse complemented.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC1103" class="line" lang="plaintext">  This only applies when :ref:`reverse complementing <reverse-complement>` was requested.</span>

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<pre style="margin: 0;"> <span id="LC1104" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC1105" class="line" lang="plaintext">For example, assume you have this input read in ``in.fasta``::</span>

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<pre style="margin: 0;"> <span id="LC1106" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1115" style="width: 35px; color: rgba(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="1117" style="width: 35px; color: rgba(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">@@ -1115,6 +1117,10 @@ Will result in this modified read::</td>

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1117

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<pre style="margin: 0;"> <span id="LC1117" class="line" lang="plaintext">    AAAA</span>

</pre>

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1116

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<td class="new_line diff-line-num" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

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<pre style="margin: 0;"> <span id="LC1118" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1117

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<td class="new_line diff-line-num" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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

<pre style="margin: 0;"> <span id="LC1119" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1120

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<pre style="margin: 0;">+<span id="LC1120" class="line" lang="plaintext">.. versionadded:: 3.3</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1121

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<pre style="margin: 0;">+<span id="LC1121" class="line" lang="plaintext">    The ``{rc}`` template variable.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1122

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<pre style="margin: 0;">+<span id="LC1122" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="1118" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="1123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1123

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

<pre style="margin: 0;">+<span id="LC1123" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="1118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1118

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<td class="new_line diff-line-num" data-linenumber="1124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1124

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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="plaintext">``--rename`` also renames paired-end reads</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1119

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<td class="new_line diff-line-num" data-linenumber="1125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1125

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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="1120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1120

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<td class="new_line diff-line-num" data-linenumber="1126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1126

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

<pre style="margin: 0;"> <span id="LC1126" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2021" style="width: 35px; color: rgba(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="2027" style="width: 35px; color: rgba(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">@@ -2021,7 +2027,8 @@ Cutadapt supports the following options to deal with ``N`` bases in your reads:</td>

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2021

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<td class="new_line diff-line-num" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2027

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<pre style="margin: 0;"> <span id="LC2027" class="line" lang="plaintext">``--max-n COUNT``</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2022" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2022

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<td class="new_line diff-line-num" data-linenumber="2028" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2028

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<pre style="margin: 0;"> <span id="LC2028" class="line" lang="plaintext">    Discard reads containing more than *COUNT* ``N`` bases. A fractional *COUNT*</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2023" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2023

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<td class="new_line diff-line-num" data-linenumber="2029" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2029

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<pre style="margin: 0;"> <span id="LC2029" class="line" lang="plaintext">    between 0 and 1 can also be given and will be treated as the proportion of</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2024" 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">

2024

</td>

<td class="new_line diff-line-num old" data-linenumber="2030" 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="LC2024" class="line" lang="plaintext">    maximally allowed ``N`` bases in the read.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2025" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2030" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2030

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<pre style="margin: 0;">+<span id="LC2030" class="line" lang="plaintext">    maximally allowed ``N`` bases in the read. For example, ``--max-n 0``</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2025" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2031" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2031

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

<pre style="margin: 0;">+<span id="LC2031" class="line" lang="plaintext">    removes all reads that contain any ``N`` bases.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2025" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2025

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<td class="new_line diff-line-num" data-linenumber="2032" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2032

</td>

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

<pre style="margin: 0;"> <span id="LC2032" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2026" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2026

</td>

<td class="new_line diff-line-num" data-linenumber="2033" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2033

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<pre style="margin: 0;"> <span id="LC2033" class="line" lang="plaintext">``--trim-n``</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2027" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2027

</td>

<td class="new_line diff-line-num" data-linenumber="2034" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2034

</td>

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<pre style="margin: 0;"> <span id="LC2034" class="line" lang="plaintext">    Remove flanking ``N`` bases from each read. That is, a read such as this::</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2185" style="width: 35px; color: rgba(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="2192" style="width: 35px; color: rgba(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">@@ -2185,7 +2192,7 @@ from the final FASTA/FASTQ output due to filtering options</td>

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<td class="old_line diff-line-num" data-linenumber="2185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2185

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<td class="new_line diff-line-num" data-linenumber="2192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2192

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<pre style="margin: 0;"> <span id="LC2192" class="line" lang="plaintext">(such as ``--minimum-length``). Which fields are output in each row</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2186

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<td class="new_line diff-line-num" data-linenumber="2193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2193

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

<pre style="margin: 0;"> <span id="LC2193" class="line" lang="plaintext">depends on whether an adapter match was found in the read or not.</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2187

</td>

<td class="new_line diff-line-num" data-linenumber="2194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2194

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

<pre style="margin: 0;"> <span id="LC2194" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num old" data-linenumber="2188" 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">

2188

</td>

<td class="new_line diff-line-num old" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC2188" class="line" lang="plaintext"><span class="idiff left right">The fields in a row that describes a match are</span>:</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="2189" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2195

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

<pre style="margin: 0;">+<span id="LC2195" class="line" lang="plaintext"><span class="idiff left right">If an adapter match was found, these fields are output in each row</span>:</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2189

</td>

<td class="new_line diff-line-num" data-linenumber="2196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2196

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

<pre style="margin: 0;"> <span id="LC2196" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2190

</td>

<td class="new_line diff-line-num" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2197

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

<pre style="margin: 0;"> <span id="LC2197" class="line" lang="plaintext">1. Read name</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2191

</td>

<td class="new_line diff-line-num" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2198

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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="plaintext">2. Number of errors</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2198" style="width: 35px; color: rgba(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="2205" style="width: 35px; color: rgba(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">@@ -2198,6 +2205,8 @@ The fields in a row that describes a match are:</td>

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<td class="old_line diff-line-num" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2198

</td>

<td class="new_line diff-line-num" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2205

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

<pre style="margin: 0;"> <span id="LC2205" class="line" lang="plaintext">9. Quality values corresponding to sequence left of the adapter match (can be empty)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2199

</td>

<td class="new_line diff-line-num" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2206

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

<pre style="margin: 0;"> <span id="LC2206" class="line" lang="plaintext">10. Quality values corresponding to sequence matched to the adapter (can be empty)</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2200

</td>

<td class="new_line diff-line-num" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2207

</td>

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

<pre style="margin: 0;"> <span id="LC2207" class="line" lang="plaintext">11. Quality values corresponding to sequence to the right of the adapter match (can be empty)</span>

</pre>

</td>

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

<td class="old_line diff-line-num new" data-linenumber="2201" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2208

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<pre style="margin: 0;">+<span id="LC2208" class="line" lang="plaintext">12. Flag indicating whether the read was reverse complemented: 1 if yes, 0 if not,</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2201" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2209

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

<pre style="margin: 0;">+<span id="LC2209" class="line" lang="plaintext">    and empty if ``--revcomp`` was not used.</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2201

</td>

<td class="new_line diff-line-num" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2210

</td>

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

<pre style="margin: 0;"> <span id="LC2210" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2202

</td>

<td class="new_line diff-line-num" data-linenumber="2211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2211

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<pre style="margin: 0;"> <span id="LC2211" class="line" lang="plaintext">The concatenation of the fields 5-7 yields the full read sequence. Column 8 identifies</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2203

</td>

<td class="new_line diff-line-num" data-linenumber="2212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2212

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<pre style="margin: 0;"> <span id="LC2212" class="line" lang="plaintext">the found adapter. `The section about named adapters <named-adapters>` describes</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2205" style="width: 35px; color: rgba(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="2214" style="width: 35px; color: rgba(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">@@ -2205,6 +2214,10 @@ how to give a name to an adapter. Adapters without a name are numbered starting</td>

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<td class="old_line diff-line-num" data-linenumber="2205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2205

</td>

<td class="new_line diff-line-num" data-linenumber="2214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2214

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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="plaintext">from 1. Fields 9-11 are empty if quality values are not available.</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2206

</td>

<td class="new_line diff-line-num" data-linenumber="2215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2215

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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="plaintext">Concatenating them yields the full sequence of quality values.</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="2207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2207

</td>

<td class="new_line diff-line-num" data-linenumber="2216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2216

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

<pre style="margin: 0;"> <span id="LC2216" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="2208" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2217

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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="plaintext">If the adapter match was found on the reverse complement of the read, fields 5 to 7</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="2208" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2218

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

<pre style="margin: 0;">+<span id="LC2218" class="line" lang="plaintext">show the reverse-complemented sequence, and fields 9-11 contain the qualities in</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2219

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

<pre style="margin: 0;">+<span id="LC2219" class="line" lang="plaintext">reversed order.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2208" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2220

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<pre style="margin: 0;">+<span id="LC2220" class="line" lang="plaintext"></span>

</pre>

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2208

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<td class="new_line diff-line-num" data-linenumber="2221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2221

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<pre style="margin: 0;"> <span id="LC2221" class="line" lang="plaintext">If no adapter was found, the format is as follows:</span>

</pre>

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2209

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2222

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<pre style="margin: 0;"> <span id="LC2222" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2210

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<td class="new_line diff-line-num" data-linenumber="2223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2223

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<pre style="margin: 0;"> <span id="LC2223" class="line" lang="plaintext">1. Read name</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2237" style="width: 35px; color: rgba(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="2250" style="width: 35px; color: rgba(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">@@ -2237,3 +2250,6 @@ a match of the 3' adapter, the string ``;2`` is added. If there are two rows, th</td>

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2237

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2250

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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="plaintext"></span>

</pre>

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2238

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<td class="new_line diff-line-num" data-linenumber="2251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2251

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<pre style="margin: 0;"> <span id="LC2251" class="line" lang="plaintext">.. versionadded:: 2.8</span>

</pre>

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2239

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2252

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<pre style="margin: 0;"> <span id="LC2252" class="line" lang="plaintext">    Linked adapters in info files work.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2240" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2253

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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="2240" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="2254" style="width: 35px; color: rgba(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="LC2254" class="line" lang="plaintext">.. versionadded:: 3.4</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="2255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

2255

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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="plaintext">    Column 12 (revcomp flag) added</span></pre>

</td>

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<br>

</li>

<li id="6677207c6fa30ac9cec19ad036ae842582159ecb">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#6677207c6fa30ac9cec19ad036ae842582159ecb"><strong>doc/installation.rst</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -129,6 +129,39 @@ system-installed packages::</td>

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129

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext">    sudo ln -s ../cutadapt/bin/cutadapt</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(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="LC131" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">Installation on Windows</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="plaintext">For some releases of Cutadapt, a single-file executable (``cutadapt.exe``)</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(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="LC136" class="line" lang="plaintext">is made available on the</span>

</pre>

</td>

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<td class="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">`GitHub releases page <https://github.com/marcelm/cutadapt/releases>`_. Try that</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">first, and if it does not work for you, please report the issue.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">To install Cutadapt manually, keep reading.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">There is no Bioconda package for Windows because Bioconda does not produce</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Windows packages. To install Cutadapt, you can use ``pip``, but because</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">Cutadapt contains components that need to be compiled, you also need to install</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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

<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">a compiler.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

146

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">1. Download a recent version (at least 3.6) of Python for Windows from</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">   <https://www.python.org/> and install it.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">2. Download and install “Build Tools for Visual Studio 2019” from</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

150

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">   <https://visualstudio.microsoft.com/downloads/#build-tools-for-visual-studio-2019>.</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">   (There are many similarly named downloads on that page, ensure you get the</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

152

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">   right one.)</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

153

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

154

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

<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">   During installation, when the dialog about which components to install pops</span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

155

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">   up, ensure that “C++ Build tools” is ticked. The download is quite big and</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

156

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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">   can take a long time.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">3. Open the command line (``cmd.exe``) and run ``py -m pip install cutadapt``.</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">4. Test whether it worked by running ``py -m cutadapt --version``. You should</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">   see the version number of Cutadapt.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">When running Cutadapt this way, you will need to remember to write</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">``py -m cutadapt`` instead of just ``cutadapt``.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext">Uninstalling</span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext">------------</span>

</pre>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>

</pre>

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<li id="5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -3,3 +3,8 @@ requires = ["setuptools", "wheel", "setuptools_scm", "cython"]</td>

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3

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3

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

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="toml"><span class="nn" style="color: #555;">[black.tool]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="toml"><span class="py">line-length</span> <span class="p">=</span> <span class="mi" style="color: #099;">100</span></span>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="toml"><span class="nn" style="color: #555;">[tool.pytest.ini_options]</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="toml"><span class="py">filterwarnings</span> <span class="p">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="toml">    <span class="s" style="color: #d14;">"error"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="toml"><span class="p">]</span></span></pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -101,7 +101,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">    <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'cutadapt = cutadapt.__main__:main_cli'</span><span class="p">]},</span></span>

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">    <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">        <span class="s" style="color: #d14;">'dnaio~=0.5.0'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python">        <span class="s" style="color: #d14;">'xopen~=1.<span class="idiff left right">0</span>.0'</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">        <span class="s" style="color: #d14;">'xopen~=1.<span class="idiff left right">1</span>.0'</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">        <span class="s" style="color: #d14;">"dataclasses>=0.8; python_version<'3.7'"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">    <span class="n" style="color: #333;">extras_require</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span></span>

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<br>

</li>

<li id="babdfe5d368a4907abadce7f9b00dfab2489185a">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#babdfe5d368a4907abadce7f9b00dfab2489185a"><strong>src/cutadapt/__main__.py</strong></a>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">cutadapt version {version}</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (C) 2010-202<span class="idiff left right">0</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (C) 2010-202<span class="idiff left right">1</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">cutadapt removes adapter sequences from high-throughput sequencing reads.</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="688" style="width: 35px; color: rgba(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="688" style="width: 35px; color: rgba(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">@@ -688,17 +688,18 @@ def pipeline_from_parsed_args(args, paired, file_opener, adapters, adapters2) -></td>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">action</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC689" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">times</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC690" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">reverse_complement</span><span class="p">,</span></span>

</pre>

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691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python">        <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">,</span>  <span class="c1" style="color: #998; font-style: italic;"># no "rc" suffix if --rename is used</span></span>

</pre>

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691

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">,</span></span>

</pre>

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692

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693

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python">    <span class="p">)</span></span>

</pre>

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693

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694

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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python"></span>

</pre>

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694

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695

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">modifier</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">modifiers_applying_to_both_ends_if_paired</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

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695

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696

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python">        <span class="n" style="color: #333;">pipeline_add</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)</span></span>

</pre>

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696

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<td class="new_line diff-line-num" data-linenumber="697" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

697

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python"></span>

</pre>

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697

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<td class="new_line diff-line-num old" data-linenumber="698" 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="LC697" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">:</span></span>

</pre>

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698

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<td class="new_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">prefix</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">suffix</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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699

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<td class="new_line diff-line-num old" data-linenumber="698" 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="LC699" class="line" lang="python">            <span class="k" style="font-weight: 600;"><span class="idiff left">rais</span>e</span> <span class="n" style="color: #333;"><span class="idiff">C</span>om<span class="idiff">mandLineError</span></span><span class="p"><span class="idiff right">(</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="700" 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">

700

</td>

<td class="new_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC700" class="line" lang="python">        <span class="idiff left">        </span><span class="s" style="color: #d14;"><span class="idiff right">"Option --rename cannot be combined with --prefix (-x) or --suffix (-y)"</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="701" 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">

701

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<td class="new_line diff-line-num old" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC701" class="line" lang="python">    <span class="idiff left">        </span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="698" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

698

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">prefix</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">suffix</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

699

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<pre style="margin: 0;">+<span id="LC699" class="line" lang="python">        <span class="k" style="font-weight: 600;"><span class="idiff left">raise</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CommandLineError</span></span><span class="p"><span class="idiff right">(</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="700" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

700

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<pre style="margin: 0;">+<span id="LC700" class="line" lang="python">            <span class="s" style="color: #d14;"><span class="idiff left">"Option --rename cannot b</span>e <span class="idiff">c</span>om<span class="idiff right">bined with --prefix (-x) or --suffix (-y)"</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

701

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<pre style="margin: 0;">+<span id="LC701" class="line" lang="python">        <span class="p"><span class="idiff left right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="702" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

702

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<pre style="margin: 0;">+<span id="LC702" class="line" lang="python">    <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rename</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">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">rename</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">"{header}"</span></span><span class="p"><span class="idiff right">:</span></span></span>

</pre>

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702

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<td class="new_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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<td class="new_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">                <span class="n" style="color: #333;">pipeline</span><span class="p">.</span><span class="n" style="color: #333;">add_paired_modifier</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndRenamer</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rename</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="781" style="width: 35px; color: rgba(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="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -781,6 +782,7 @@ def add_adapter_cutter(</td>

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<td class="old_line diff-line-num" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

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<td class="new_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python">    <span class="n" style="color: #333;">action</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

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<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python">    <span class="n" style="color: #333;">times</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python">    <span class="n" style="color: #333;">reverse_complement</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

785

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

<pre style="margin: 0;">+<span id="LC785" class="line" lang="python">    <span class="n" style="color: #333;">add_rc_suffix</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

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<td class="new_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python">    <span class="n" style="color: #333;">allow_index</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

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<td class="new_line diff-line-num" data-linenumber="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

787

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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

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<td class="new_line diff-line-num" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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

<pre style="margin: 0;"> <span id="LC788" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pair_adapters</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="808" style="width: 35px; color: rgba(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="810" style="width: 35px; color: rgba(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">@@ -808,7 +810,8 @@ def add_adapter_cutter(</td>

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<td class="old_line diff-line-num" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

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<td class="new_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">adapter_cutter</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

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<td class="new_line diff-line-num" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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

<pre style="margin: 0;"> <span id="LC811" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

</td>

<td class="new_line diff-line-num" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

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

<pre style="margin: 0;"> <span id="LC812" class="line" lang="python">                <span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReverseComplementer</span><span class="p">(</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="811" 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">

811

</td>

<td class="new_line diff-line-num old" data-linenumber="813" 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="LC811" class="line" lang="python">                    <span class="n" style="color: #333;">adapter_cutter</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

813

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<pre style="margin: 0;">+<span id="LC813" class="line" lang="python">                    <span class="n" style="color: #333;">adapter_cutter</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="812" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

814

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<pre style="margin: 0;">+<span id="LC814" class="line" lang="python">                    <span class="n" style="color: #333;">rc_suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">" rc"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">add_rc_suffix</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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812

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<td class="new_line diff-line-num" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python">                <span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Union[AdapterCutter,ReverseComplementer]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

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<td class="new_line diff-line-num" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

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<pre style="margin: 0;"> <span id="LC816" 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="LC817" class="line" lang="python">                <span class="n" style="color: #333;">modifier</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_cutter</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="860" style="width: 35px; color: rgba(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="863" style="width: 35px; color: rgba(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">@@ -860,9 +863,7 @@ def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:</td>

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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Setup logging only if there are not already any handlers (can happen when</span></span>

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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># this function is being called externally such as from unit tests)</span></span>

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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">handlers</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># If results are to be sent to stdout, logging needs to go to stderr</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python">        <span class="n" style="color: #333;">log_to_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">paired_output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="865" 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="LC865" class="line" lang="python">        <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">log_to_stdout</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="866" style="width: 35px; color: rgba(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="LC866" class="line" lang="python">        <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">log_to_stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_any_output_stdout</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="867" style="width: 35px; color: rgba(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="LC867" class="line" lang="python">            <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'minimal'</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC868" class="line" lang="python">    <span class="n" style="color: #333;">log_header</span><span class="p">(</span><span class="n" style="color: #333;">cmdlineargs</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC869" class="line" lang="python">    <span class="n" style="color: #333;">profiler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">setup_profiler_if_requested</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">profile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="879" style="width: 35px; color: rgba(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="880" style="width: 35px; color: rgba(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">@@ -879,8 +880,8 @@ def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:</td>

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<pre style="margin: 0;"> <span id="LC880" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="880" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="881" style="width: 35px; color: rgba(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="LC881" class="line" lang="python">    <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cores</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC882" class="line" lang="python">    <span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOpener</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC882" class="line" lang="python">        <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left">0</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">else</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">)</span></span>

</pre>

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883

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<pre style="margin: 0;">-<span id="LC883" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">isatty</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="883" style="width: 35px; color: rgba(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="LC883" class="line" lang="python">        <span class="n" style="color: #333;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">estimate_compression_threads</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="884" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

884

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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">isatty</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="idiff left"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">not</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">debug</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC885" class="line" lang="python">        <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Progress</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="885" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

885

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<td class="new_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(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="LC886" 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="old_line diff-line-num" data-linenumber="886" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="887" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

887

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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python">        <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DummyProgress</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="944" style="width: 35px; color: rgba(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="945" style="width: 35px; color: rgba(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">@@ -944,7 +945,7 @@ def setup_runner(</td>

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<td class="new_line diff-line-num" data-linenumber="945" style="width: 35px; color: rgba(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="LC945" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="946" style="width: 35px; color: rgba(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="LC946" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="947" style="width: 35px; color: rgba(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="LC947" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="947" 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="new_line diff-line-num old" data-linenumber="948" 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="LC947" class="line" lang="python">                <span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">inpaths</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="948" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

948

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<pre style="margin: 0;">+<span id="LC948" class="line" lang="python">                <span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">inpaths</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">file_opener</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="949" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

949

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<pre style="margin: 0;"> <span id="LC949" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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949

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<td class="new_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

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<pre style="margin: 0;"> <span id="LC950" class="line" lang="python">            <span class="n" style="color: #333;">infiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">inpaths</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="950" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

950

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<td class="new_line diff-line-num" data-linenumber="951" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

951

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<pre style="margin: 0;"> <span id="LC951" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">SerialPipelineRunner</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="972" style="width: 35px; color: rgba(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="973" style="width: 35px; color: rgba(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">@@ -972,5 +973,26 @@ def warn_if_en_dashes(args):</td>

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<td class="old_line diff-line-num" data-linenumber="972" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

972

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<td class="new_line diff-line-num" data-linenumber="973" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

973

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<pre style="margin: 0;"> <span id="LC973" class="line" lang="python">            <span class="p">)</span></span>

</pre>

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973

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<td class="new_line diff-line-num" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

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<pre style="margin: 0;"> <span id="LC974" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

974

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<td class="new_line diff-line-num" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

975

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<pre style="margin: 0;"> <span id="LC975" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

976

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<pre style="margin: 0;">+<span id="LC976" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_compression_threads</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">]:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="977" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

977

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

<pre style="margin: 0;">+<span id="LC977" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="978" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

978

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

<pre style="margin: 0;">+<span id="LC978" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="979" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

979

</td>

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

<pre style="margin: 0;">+<span id="LC979" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="980" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

980

</td>

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

<pre style="margin: 0;">+<span id="LC980" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_any_output_stdout</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="981" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

981

</td>

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

<pre style="margin: 0;">+<span id="LC981" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">([</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="982" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

982

</td>

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

<pre style="margin: 0;">+<span id="LC982" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="983" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

983

</td>

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

<pre style="margin: 0;">+<span id="LC983" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="984" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

984

</td>

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

<pre style="margin: 0;">+<span id="LC984" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">paired_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="985" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

985

</td>

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

<pre style="margin: 0;">+<span id="LC985" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">untrimmed_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="986" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

986

</td>

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

<pre style="margin: 0;">+<span id="LC986" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">untrimmed_paired_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="987" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

987

</td>

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

<pre style="margin: 0;">+<span id="LC987" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">too_short_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="988" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

988

</td>

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

<pre style="margin: 0;">+<span id="LC988" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">too_short_paired_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="989" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

989

</td>

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

<pre style="margin: 0;">+<span id="LC989" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">too_long_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="990" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

990

</td>

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

<pre style="margin: 0;">+<span id="LC990" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">too_long_paired_output</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="991" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

991

</td>

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

<pre style="margin: 0;">+<span id="LC991" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">rest_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="992" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

992

</td>

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

<pre style="margin: 0;">+<span id="LC992" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">info_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="993" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

993

</td>

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

<pre style="margin: 0;">+<span id="LC993" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">wildcard_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="994" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

994

</td>

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

<pre style="margin: 0;">+<span id="LC994" class="line" lang="python">    <span class="p">])</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="995" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

995

</td>

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

<pre style="margin: 0;">+<span id="LC995" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="975" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="996" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

996

</td>

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

<pre style="margin: 0;">+<span id="LC996" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="975" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

975

</td>

<td class="new_line diff-line-num" data-linenumber="997" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

997

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

<pre style="margin: 0;"> <span id="LC997" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># pragma: no cover</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="976" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

976

</td>

<td class="new_line diff-line-num" data-linenumber="998" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

998

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

<pre style="margin: 0;"> <span id="LC998" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="n" style="color: #333;">main_cli</span><span class="p">())</span></span></pre>

</td>

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<br>

</li>

<li id="ecaf81c67bfb6c86fbef95a99558f4bec3b0c983">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#ecaf81c67bfb6c86fbef95a99558f4bec3b0c983"><strong>src/cutadapt/_align.pyi</strong></a>

<hr>

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

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

<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">@@ -4,7 +4,7 @@ class DPMatrix:</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="plaintext">    m: int</span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">    n: int</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">    def __init__(self, reference: str, query: str): ...</span>

</pre>

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

7

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<td class="new_line diff-line-num old" data-linenumber="7" 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="LC7" class="line" lang="plaintext">    def set_entry(self, i: int, j: int, cost: int): ...</span>

</pre>

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

</td>

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

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">    def set_entry(self, i: int, j: int, cost: int)<span class="idiff left right"> -> None</span>: ...</span>

</pre>

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

8

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

8

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">    def __str__(self) -> str: ...</span>

</pre>

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<td class="old_line diff-line-num" 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

</td>

<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8fb347891ec0a40b16ef2bdbe361f823e12aa016">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#8fb347891ec0a40b16ef2bdbe361f823e12aa016"><strong>src/cutadapt/adapters.py</strong></a>

<hr>

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

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,6 +49,7 @@ class EndStatistics:</td>

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<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span>  <span class="c1" style="color: #998; font-style: italic;"># type: str</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">effective_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">effective_length</span>  <span class="c1" style="color: #998; font-style: italic;"># type: int</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">has_wildcards</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">adapter_wildcards</span>  <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">allows_partial_matches</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">allows_partial_matches</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># self.errors[l][e] == n iff n times a sequence of length l matching at e errors was removed</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="n" style="color: #333;">returns_defaultdict_int</span><span class="p">)</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Dict[int, Dict[int, int]]</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">adjacent_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'A'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'C'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'G'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">'T'</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -395,6 +396,8 @@ class SingleAdapter(Adapter, ABC):</td>

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"><span class="s" style="color: #d14;">        unique number.</span></span>

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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python">    <span class="n" style="color: #333;">allows_partial_matches</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</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="LC400" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">        <span class="n" style="color: #333;">sequence</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="617" style="width: 35px; color: rgba(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="620" style="width: 35px; color: rgba(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">@@ -617,6 +620,7 @@ class PrefixAdapter(NonInternalFrontAdapter):</td>

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python">    <span class="s" style="color: #d14;">"""An anchored 5' adapter"""</span></span>

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"></span>

</pre>

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619

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<td class="new_line diff-line-num" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python">    <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"anchored 5'"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="620" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="623" style="width: 35px; color: rgba(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="LC623" class="line" lang="python">    <span class="n" style="color: #333;">allows_partial_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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620

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624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_aligner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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622

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<td class="new_line diff-line-num" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

626

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<pre style="margin: 0;"> <span id="LC626" 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="p">.</span><span class="n" style="color: #333;">indels</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># TODO or if error rate allows 0 errors anyway</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="635" style="width: 35px; color: rgba(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="639" style="width: 35px; color: rgba(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">@@ -635,6 +639,7 @@ class SuffixAdapter(NonInternalBackAdapter):</td>

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635

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639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python">    <span class="s" style="color: #d14;">"""An anchored 3' adapter"""</span></span>

</pre>

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636

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

637

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<td class="new_line diff-line-num" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python">    <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"anchored 3'"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC642" class="line" lang="python">    <span class="n" style="color: #333;">allows_partial_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

638

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<td class="new_line diff-line-num" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="639" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="644" style="width: 35px; color: rgba(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="LC644" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_aligner</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<td class="new_line diff-line-num" data-linenumber="645" style="width: 35px; color: rgba(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="LC645" 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="p">.</span><span class="n" style="color: #333;">indels</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># TODO or if error rate allows 0 errors anyway</span></span>

</pre>

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<br>

</li>

<li id="98e6d8e6e9db700c1f73b5678eae963cb214cbc9">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#98e6d8e6e9db700c1f73b5678eae963cb214cbc9"><strong>src/cutadapt/align.py</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,8 @@ __all__ = [</td>

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8

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

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python">    <span class="s" style="color: #d14;">'edit_distance'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="p">]</span></span>

</pre>

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10

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<td class="new_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

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

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

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt._align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Aligner</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixComparer</span><span class="p">,</span> <span class="n" style="color: #333;">SuffixComparer</span></span>

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

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># flags for global alignment</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">@@ -28,7 +30,7 @@ STOP_WITHIN_SEQ2 = 8</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="n" style="color: #333;">SEMIGLOBAL</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">START_WITHIN_SEQ1</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">START_WITHIN_SEQ2</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">STOP_WITHIN_SEQ1</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">STOP_WITHIN_SEQ2</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">edit_distance</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">edit_distance</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">int</span></span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">    Return the edit distance between the strings s and t.</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">    The edit distance is the sum of the numbers of insertions, deletions,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="54" style="width: 35px; color: rgba(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">@@ -54,7 +56,7 @@ def edit_distance(s: str, t: str):</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">costs</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

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

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

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hamming_sphere</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hamming_sphere</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</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="n" style="color: #333;"><span class="idiff">Iterator</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff right">]</span>:</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">    Yield all strings t for which the hamming distance between s and t is exactly k,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;">    assuming the alphabet is A, C, G, T.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" style="width: 35px; color: rgba(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="81" style="width: 35px; color: rgba(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">@@ -79,7 +81,7 @@ def hamming_sphere(s, k):</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">                <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">y</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="83" style="width: 35px; color: rgba(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="LC83" class="line" lang="python"></span>

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<td class="new_line diff-line-num old" data-linenumber="84" 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="LC82" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hamming_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">hamming_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">k</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</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="n" style="color: #333;"><span class="idiff">Iterator</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(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="LC85" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="86" style="width: 35px; color: rgba(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="LC86" class="line" lang="python"><span class="s" style="color: #d14;">    Find all strings t for which the hamming distance between s and t is at most k,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="85" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="87" style="width: 35px; color: rgba(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="LC87" class="line" lang="python"><span class="s" style="color: #d14;">    assuming the alphabet is A, C, G, T.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,7 +95,7 @@ def hamming_environment(s, k):</td>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">e</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">naive_edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">naive_edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span><span class="idiff left"> </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">Iterator</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff right">]</span>:</span></span>

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<td class="new_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    Apply all possible edits up to edit distance k to string s.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="s" style="color: #d14;">    A string may be returned more than once.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="114" style="width: 35px; color: rgba(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="116" style="width: 35px; color: rgba(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">@@ -114,7 +116,7 @@ def naive_edit_environment(s: str, k: int):</td>

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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(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="LC116" class="line" lang="python">            <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">s</span><span class="p">[:</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>

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<td class="new_line diff-line-num" data-linenumber="117" style="width: 35px; color: rgba(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="LC117" class="line" lang="python"></span>

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<td class="new_line diff-line-num" data-linenumber="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="117" 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="new_line diff-line-num old" data-linenumber="119" 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="LC117" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span><span class="idiff left"> </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">Iterator</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(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="LC120" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="121" style="width: 35px; color: rgba(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="LC121" class="line" lang="python"><span class="s" style="color: #d14;">    Find all strings t for which the edit distance between s and t is at most k,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="120" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="122" style="width: 35px; color: rgba(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="LC122" class="line" lang="python"><span class="s" style="color: #d14;">    assuming the alphabet is A, C, G, T.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -134,7 +136,7 @@ def edit_environment(s: str, k: int):</td>

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<td class="new_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span></span>

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<td class="old_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">slow_edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(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="LC139" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">slow_edit_environment</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span><span class="idiff left"> </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">Iterator</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;">    Find all strings t for which the edit distance between s and t is at most k,</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;">    assuming the alphabet is A, C, G, T.</span></span>

</pre>

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<br>

</li>

<li id="6ed465db6839a69141086c2acf1dc01a8b17a981">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#6ed465db6839a69141086c2acf1dc01a8b17a981"><strong>src/cutadapt/filters.py</strong></a>

<hr>

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<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">@@ -23,6 +23,8 @@ from .modifiers import ModificationInfo</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Constants used when returning from a Filter’s __call__ method to improve</span></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># readability (it is unintuitive that "return True" means "discard the read").</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">reverse_complemented_sequence</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="n" style="color: #333;">DISCARD</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="LC29" class="line" lang="python"><span class="n" style="color: #333;">KEEP</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(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="120" style="width: 35px; color: rgba(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">@@ -118,7 +120,7 @@ class PairedNoFilter(PairedEndFilterWithStatistics):</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="121" 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="new_line diff-line-num old" data-linenumber="123" 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="LC121" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Redirector</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Redirector</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;">    Redirect discarded reads to the given writer. This is for single-end reads.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -137,12 +139,11 @@ class Redirector(SingleEndFilterWithStatistics):</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>

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<td class="new_line diff-line-num" 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="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>

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<td class="new_line diff-line-num" 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="python"></span>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="python"></span>

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

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

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedRedirector</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" 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="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedRedirector</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;">    Redirect paired-end reads matching a filtering criterion to a writer.</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;">    Different filtering styles are supported, differing by which of the</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="196" style="width: 35px; color: rgba(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">@@ -195,7 +196,6 @@ class PairedRedirector(PairedEndFilterWithStatistics):</td>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -416,16 +416,21 @@ class WildcardFileWriter(SingleEndFilter):</td>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InfoFileWriter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC419" class="line" lang="python">    <span class="n" style="color: #333;">RC_MAP</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="bp" style="color: #999;">None</span><span class="p">:</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="s" style="color: #d14;">"1"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span> <span class="s" style="color: #d14;">"0"</span><span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>

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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python">        <span class="n" style="color: #333;">current_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">original_read</span></span>

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<td class="new_line diff-line-num new" data-linenumber="426" style="width: 35px; color: rgba(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="LC426" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">is_rc</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python">            <span class="n" style="color: #333;">current_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_complemented_sequence</span><span class="p">(</span><span class="n" style="color: #333;">current_read</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="428" style="width: 35px; color: rgba(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="LC428" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">info_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">get_info_records</span><span class="p">(</span><span class="n" style="color: #333;">current_read</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># info_record[0] is the read name suffix</span></span>

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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">RC_MAP</span><span class="p">[</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">is_rc</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python">                        <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python">                <span class="n" style="color: #333;">current_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">.</span><span class="n" style="color: #333;">trimmed</span><span class="p">(</span><span class="n" style="color: #333;">current_read</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC435" 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="LC436" class="line" lang="python">            <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span></span>

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<br>

</li>

<li id="7107bed35fcb7c2440b754bf9d882e70c6ceb8ae">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae"><strong>src/cutadapt/log.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">@@ -30,7 +30,7 @@ class NiceFormatter(logging.Formatter):</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">stdout</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Fals</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">log_to_stderr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Tru</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">    Attach handler to the global logger object</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,7 +39,7 @@ def setup_logging(logger, stdout=False, minimal=False, quiet=False, debug=0):</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># INFO level (and the ERROR level would give us an 'ERROR:' prefix).</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">addLevelName</span><span class="p">(</span><span class="n" style="color: #333;">REPORT</span><span class="p">,</span> <span class="s" style="color: #d14;">'REPORT'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python">    <span class="n" style="color: #333;">stream_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CrashingHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">std<span class="idiff left">out</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff">stdout</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">std<span class="idiff right">err</span></span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">    <span class="n" style="color: #333;">stream_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CrashingHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">std<span class="idiff left">err</span></span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff">log_to_stderr</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">std<span class="idiff right">out</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">    <span class="n" style="color: #333;">stream_handler</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">NiceFormatter</span><span class="p">())</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># debug overrides quiet overrides minimal</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<li id="a44086ebe255bc0df91ea1d82811c828e6f5e324">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#a44086ebe255bc0df91ea1d82811c828e6f5e324"><strong>src/cutadapt/modifiers.py</strong></a>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"><span class="s" style="color: #d14;">    - {cut_prefix} -- prefix removed by UnconditionalCutter (with positive length argument)</span></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"><span class="s" style="color: #d14;">    - {cut_suffix} -- suffix removed by UnconditionalCutter (with negative length argument)</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;">    - {adapter_name} -- name of the *last* adapter match or no_adapter if there was none</span></span>

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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;">    - {rc} -- the string 'rc' if the read was reverse complemented (with --revcomp) or '' otherwise</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python">    <span class="n" style="color: #333;">variables</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">        <span class="s" style="color: #d14;">"header"</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -445,6 +446,7 @@ class Renamer(SingleEndModifier):</td>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">        <span class="s" style="color: #d14;">"cut_prefix"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python">        <span class="s" style="color: #d14;">"cut_suffix"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python">        <span class="s" style="color: #d14;">"adapter_name"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC449" class="line" lang="python">        <span class="s" style="color: #d14;">"rc"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python">    <span class="p">}</span></span>

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<td class="new_line diff-line-num" data-linenumber="451" style="width: 35px; color: rgba(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="LC451" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">template</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="455" style="width: 35px; color: rgba(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="457" style="width: 35px; color: rgba(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">@@ -455,6 +457,9 @@ class Renamer(SingleEndModifier):</td>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">raise_if_invalid_variable</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_tokens</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">variables</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">template</span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="460" style="width: 35px; color: rgba(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="LC460" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC461" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="sa">f</span><span class="s" style="color: #d14;">"Renamer('</span><span class="si" style="color: #d14;">{</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_template</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;">')"</span></span>

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<pre style="margin: 0;">+<span id="LC462" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

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<td class="new_line diff-line-num" data-linenumber="464" style="width: 35px; color: rgba(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="LC464" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">raise_if_invalid_variable</span><span class="p">(</span><span class="n" style="color: #333;">tokens</span><span class="p">:</span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">Token</span><span class="p">],</span> <span class="n" style="color: #333;">allowed</span><span class="p">:</span> <span class="n" style="color: #333;">Set</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">])</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="465" style="width: 35px; color: rgba(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="LC465" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">token</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tokens</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="484" style="width: 35px; color: rgba(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="489" style="width: 35px; color: rgba(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">@@ -484,6 +489,7 @@ class Renamer(SingleEndModifier):</td>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python">            <span class="n" style="color: #333;">cut_prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">cut_prefix</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">cut_prefix</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

485

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<td class="new_line diff-line-num" data-linenumber="490" style="width: 35px; color: rgba(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="LC490" class="line" lang="python">            <span class="n" style="color: #333;">cut_suffix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">cut_suffix</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">cut_suffix</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="486" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

486

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<td class="new_line diff-line-num" data-linenumber="491" style="width: 35px; color: rgba(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="LC491" class="line" lang="python">            <span class="n" style="color: #333;">adapter_name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">matches</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"no_adapter"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="492" style="width: 35px; color: rgba(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="LC492" class="line" lang="python">            <span class="n" style="color: #333;">rc</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rc"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">is_rc</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

495

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="512" style="width: 35px; color: rgba(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="518" style="width: 35px; color: rgba(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">@@ -512,9 +518,8 @@ class PairedEndRenamer(PairedEndModifier):</td>

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"></span>

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519

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>

</pre>

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520

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_allowed_variables</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Set</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]:</span></span>

</pre>

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515

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<td class="new_line diff-line-num old" data-linenumber="521" 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="LC515" class="line" lang="python">        <span class="n" style="color: #333;">allowed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Renamer</span><span class="p">.</span><span class="n" style="color: #333;">variables</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python">        <span class="n" style="color: #333;">allowed</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"rn"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Renamer</span><span class="p">.</span><span class="n" style="color: #333;">variables</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">{</span><span class="s" style="color: #d14;">"id"</span><span class="p">}:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="521" style="width: 35px; color: rgba(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="LC521" class="line" lang="python">        <span class="n" style="color: #333;">allowed</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Renamer</span><span class="p">.</span><span class="n" style="color: #333;">variables</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">{</span><span class="s" style="color: #d14;">"rc"</span><span class="p">})</span> <span class="o" style="font-weight: 600;">|</span> <span class="p">{</span><span class="s" style="color: #d14;">"rn"</span><span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="522" style="width: 35px; color: rgba(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="LC522" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">Renamer</span><span class="p">.</span><span class="n" style="color: #333;">variables</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">{</span><span class="s" style="color: #d14;">"id"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rc"</span><span class="p">}:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC523" class="line" lang="python">            <span class="n" style="color: #333;">allowed</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"r1."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python">            <span class="n" style="color: #333;">allowed</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="s" style="color: #d14;">"r2."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">v</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">allowed</span></span>

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<br>

</li>

<li id="12b6e14dcfabba52d86396a9e2818f75b0c0c8d5">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5"><strong>src/cutadapt/parser.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -340,6 +340,8 @@ class AdapterParser:</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">        <span class="n" style="color: #333;">adapter_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">aspec</span><span class="p">.</span><span class="n" style="color: #333;">adapter_class</span><span class="p">()</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Type[Adapter]</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">aspec</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'anywhere'</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">adapter_class</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">FrontAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">BackAdapter</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python">            <span class="n" style="color: #333;">aspec</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'force_anywhere'</span><span class="p">]</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="LC343" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'required'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">aspec</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"'required' and 'optional' can only be used within linked adapters"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">        <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">default_parameters</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">        <span class="n" style="color: #333;">parameters</span><span class="p">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">aspec</span><span class="p">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">adapter_class</span><span class="p">(</span></span>

</pre>

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<li id="1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8"><strong>src/cutadapt/pipeline.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,6 @@ import multiprocessing.connection</td>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing.connection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Connection</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">traceback</span></span>

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

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<td class="new_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">xopen</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">xopen</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span> <span class="n" style="color: #333;">FileOpener</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="530" style="width: 35px; color: rgba(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="529" style="width: 35px; color: rgba(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">@@ -530,7 +529,7 @@ class ReaderProcess(Process):</td>

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530

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python"><span class="s" style="color: #d14;">    and finally sends the stop token -1 ("poison pills") to all connections.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">],</span> <span class="n" style="color: #333;">connections</span><span class="p">,</span> <span class="n" style="color: #333;">queue</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">,</span> <span class="n" style="color: #333;">stdin_fd</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="534" style="width: 35px; color: rgba(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="LC532" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">],</span> <span class="n" style="color: #333;"><span class="idiff left">opener</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">FileOpener</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">connections</span><span class="p">,</span> <span class="n" style="color: #333;">queue</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">,</span> <span class="n" style="color: #333;">stdin_fd</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"><span class="s" style="color: #d14;">        queue -- a Queue of worker indices. A worker writes its own index into this</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python"><span class="s" style="color: #d14;">            queue to notify the reader that it is ready to receive more data.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="543" style="width: 35px; color: rgba(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="542" style="width: 35px; color: rgba(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">@@ -543,15 +542,16 @@ class ReaderProcess(Process):</td>

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queue</span></span>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer_size</span></span>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stdin_fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stdin_fd</span></span>

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<pre style="margin: 0;">+<span id="LC545" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opener</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stdin_fd</span> <span class="o" style="font-weight: 600;">!=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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549

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549

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<td class="new_line diff-line-num" data-linenumber="550" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

550

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">fdopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stdin_fd</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<td class="new_line diff-line-num" data-linenumber="551" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

551

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="552" 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">

552

</td>

<td class="new_line diff-line-num old" data-linenumber="552" 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="LC552" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="553" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="552" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

552

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<pre style="margin: 0;">+<span id="LC552" class="line" lang="python">            <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_opener</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

553

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<td class="new_line diff-line-num" data-linenumber="553" style="width: 35px; color: rgba(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="LC553" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="554" 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">

554

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<td class="new_line diff-line-num old" data-linenumber="554" 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="LC554" class="line" lang="python">                    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="555" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="554" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

554

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python">                    <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_opener</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="s" style="color: #d14;">'rb'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f2</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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<td class="new_line diff-line-num" data-linenumber="555" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

555

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">chunk_index</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">chunk1</span><span class="p">,</span> <span class="n" style="color: #333;">chunk2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<td class="new_line diff-line-num" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python">                                <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="n" style="color: #333;">read_paired_chunks</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<td class="new_line diff-line-num" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">                            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">send_to_worker</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</span><span class="p">,</span> <span class="n" style="color: #333;">chunk1</span><span class="p">,</span> <span class="n" style="color: #333;">chunk2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="740" style="width: 35px; color: rgba(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="740" style="width: 35px; color: rgba(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">@@ -740,6 +740,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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740

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<td class="new_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">        <span class="n" style="color: #333;">pipeline</span><span class="p">:</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="new_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

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<pre style="margin: 0;"> <span id="LC741" class="line" lang="python">        <span class="n" style="color: #333;">infiles</span><span class="p">:</span> <span class="n" style="color: #333;">InputPaths</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<td class="new_line diff-line-num" data-linenumber="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

742

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<pre style="margin: 0;"> <span id="LC742" class="line" lang="python">        <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

743

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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python">        <span class="n" style="color: #333;">opener</span><span class="p">:</span> <span class="n" style="color: #333;">FileOpener</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python">        <span class="n" style="color: #333;">progress</span><span class="p">:</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="745" style="width: 35px; color: rgba(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="LC745" class="line" lang="python">        <span class="n" style="color: #333;">n_workers</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python">        <span class="n" style="color: #333;">buffer_size</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">1024</span><span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">2</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(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="749" style="width: 35px; color: rgba(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">@@ -748,8 +749,9 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<pre style="margin: 0;"> <span id="LC749" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_n_workers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_workers</span></span>

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<td class="new_line diff-line-num" data-linenumber="750" style="width: 35px; color: rgba(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="LC750" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_need_work_queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Queue</span><span class="p">()</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Queue</span></span>

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer_size</span></span>

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751

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<td class="new_line diff-line-num old" data-linenumber="752" 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="LC751" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_assign_input</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">interleaved</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC752" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfiles</span></span>

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<td class="new_line diff-line-num new" data-linenumber="753" style="width: 35px; color: rgba(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="LC753" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opener</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="754" style="width: 35px; color: rgba(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="LC754" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_assign_input</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">interleaved</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="755" style="width: 35px; color: rgba(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="LC755" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC756" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assign_input</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="768" style="width: 35px; color: rgba(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="770" style="width: 35px; color: rgba(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">@@ -768,7 +770,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># This happens during tests: pytest sets sys.stdin to an object</span></span>

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># that does not have a file descriptor.</span></span>

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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python">            <span class="n" style="color: #333;">fileno</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC771" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReaderProcess</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">connw</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

773

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<pre style="margin: 0;">+<span id="LC773" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ReaderProcess</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_opener</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">connw</span><span class="p">,</span></span>

</pre>

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772

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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_need_work_queue</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_buffer_size</span><span class="p">,</span> <span class="n" style="color: #333;">fileno</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(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="LC775" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span><span class="p">.</span><span class="n" style="color: #333;">daemon</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="776" style="width: 35px; color: rgba(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="LC776" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -798,8 +800,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>

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<pre style="margin: 0;"> <span id="LC800" class="line" lang="python">        <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span>  <span class="c1" style="color: #998; font-style: italic;"># A running total of the number of processed reads (for progress indicator)</span></span>

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<pre style="margin: 0;"> <span id="LC801" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">connections</span><span class="p">:</span></span>

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802

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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python">            <span class="n" style="color: #333;">ready_connections</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">(</span><span class="n" style="color: #333;">connections</span><span class="p">)</span></span>

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801

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<td class="new_line diff-line-num old" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC801" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">connection</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ready_connections</span><span class="p">:</span></span>

</pre>

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802

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<pre style="margin: 0;">-<span id="LC802" class="line" lang="python">                <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">Connection</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

803

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<pre style="margin: 0;">+<span id="LC803" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">connection</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ready_connections</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># type: Any</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="804" style="width: 35px; color: rgba(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="LC804" class="line" lang="python">                <span class="n" style="color: #333;">chunk_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chunk_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="805" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="806" style="width: 35px; color: rgba(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="LC806" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># the worker is done</span></span>

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<br>

</li>

<li id="0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de"><strong>src/cutadapt/report.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="210" style="width: 35px; color: rgba(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="210" style="width: 35px; color: rgba(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">@@ -210,18 +210,21 @@ class Statistics:</td>

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210

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">adapter_statistics</span><span class="p">:</span> <span class="n" style="color: #333;">EndStatistics</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python">    <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_statistics</span><span class="p">.</span><span class="n" style="color: #333;">effective_length</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python">    <span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_statistics</span><span class="p">.</span><span class="n" style="color: #333;">max_error_rate</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python">    <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python">    <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">errors</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">        <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">error_rate</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{}-{} bp: {}; "</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">        <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span></span>

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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{} bp: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter_statistics</span><span class="p">.</span><span class="n" style="color: #333;">allows_partial_matches</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python">        <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">errors</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python">            <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">error_rate</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python">            <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{}-{} bp: {}; "</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">            <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">r</span></span>

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">length</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python">            <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{} bp: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC222" 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="LC223" class="line" lang="python">            <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{}-{} bp: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC224" 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="LC222" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;"><span class="idiff left">+</span>=</span> <span class="s" style="color: #d14;"><span class="idiff">"{}-{} bp: {}"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prev</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">)<span class="idiff right">)</span></span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">        <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa"><span class="idiff left">f</span></span><span class="s" style="color: #d14;"><span class="idiff">" </span></span><span class="si" style="color: #d14;"><span class="idiff">{</span></span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">length</span><span class="p">)</span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s" style="color: #d14;"><span class="idiff right">"</span></span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"No. of allowed errors:</span><span class="se" style="color: #d14;"><span class="idiff left right">\n</span></span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"No. of allowed errors:"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="229" style="width: 35px; color: rgba(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="LC229" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="230" style="width: 35px; color: rgba(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="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">histogram</span><span class="p">(</span><span class="n" style="color: #333;">end_statistics</span><span class="p">:</span> <span class="n" style="color: #333;">EndStatistics</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">gc_content</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="303" style="width: 35px; color: rgba(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="306" style="width: 35px; color: rgba(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">@@ -303,7 +306,8 @@ def full_report(stats: Statistics, time: float, gc_content: float) -> str:  # no</td>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print report to standard output."""</span></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"No reads processed!"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="309" style="width: 35px; color: rgba(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="LC309" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python">        <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1E-6</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">    <span class="n" style="color: #333;">sio</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_s</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<br>

</li>

<li id="af95dfcb30a51908f338d0fd6a196b9e4c108046">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#af95dfcb30a51908f338d0fd6a196b9e4c108046"><strong>src/cutadapt/utils.py</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,6 +42,23 @@ def available_cpu_count():</td>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">()</span></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">    Run 'func' (which should be some kind of open() function and return its result.</span></span>

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;">    If "Too many open files" occurs, increase limit and try again.</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">        <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="p">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>

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

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

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">            <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Too many open files, attempting to raise soft limit"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">            <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">            <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">func</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="59" style="width: 35px; color: rgba(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="LC59" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">raise_open_files_limit</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">resource</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="91" style="width: 35px; color: rgba(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="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,6 +108,8 @@ class Progress:</td>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">            <span class="n" style="color: #333;">delta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_n</span></span>

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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">delta</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

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<td class="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(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="LC111" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">time_delta</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">_final</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">time_delta</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_every</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="163" style="width: 35px; color: rgba(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="182" style="width: 35px; color: rgba(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">@@ -163,8 +182,12 @@ class FileOpener:</td>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">threads</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">xopen</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>

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<td class="new_line diff-line-num old" data-linenumber="185" 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="LC166" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Opening file '%s', mode '%s' with xopen"</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="185" 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="LC167" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">compresslevel</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="185" style="width: 35px; color: rgba(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="LC185" class="line" lang="python">        <span class="n" style="color: #333;">threads</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">threads</span> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"w"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mode</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">0</span></span>

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<td class="new_line diff-line-num new" data-linenumber="186" style="width: 35px; color: rgba(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="LC186" class="line" lang="python">        <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open_raise_limit</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python">            <span class="n" style="color: #333;">xopen</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">compresslevel</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threads</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python">        <span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="189" style="width: 35px; color: rgba(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="LC189" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Opening '%s', mode '%s' with xopen resulted in %s"</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="190" style="width: 35px; color: rgba(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="LC190" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">xopen_or_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python">        <span class="s" style="color: #d14;">"""Return opened file or None if the path is None"""</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="181" style="width: 35px; color: rgba(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">@@ -181,22 +204,15 @@ class FileOpener:</td>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dnaio_open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Opening file '%s', mode '%s' with dnaio"</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'mode'</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python">        <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"opener"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">xopen</span></span>

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<td class="new_line diff-line-num old" data-linenumber="208" 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="LC186" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="208" style="width: 35px; color: rgba(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="LC208" class="line" lang="python">        <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="209" style="width: 35px; color: rgba(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="LC209" class="line" lang="python">        <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Opening %r, mode '%s' with dnaio resulted in %s"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="210" style="width: 35px; color: rgba(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="LC210" class="line" lang="python">            <span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'mode'</span><span class="p">],</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(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="LC211" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">dnaio_open_raise_limit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="214" style="width: 35px; color: rgba(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="LC214" class="line" lang="python">        <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;">        Open a FASTA/FASTQ file for writing. If it fails because the number of open files</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;">        would be exceeded, try to raise the soft limit and re-try.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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193

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC193" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="194" 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">

194

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC194" class="line" lang="python">            <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="195" 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">

195

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC195" class="line" lang="python">        <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="196" 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">

196

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC196" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="p">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span>  <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" 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">

197

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC197" class="line" lang="python">                <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Too many open files, attempting to raise soft limit"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" 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">

198

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC198" class="line" lang="python">                <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" 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">

199

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC199" class="line" lang="python">                <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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200

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC200" 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="old_line diff-line-num old" data-linenumber="201" 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">

201

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<td class="new_line diff-line-num old" data-linenumber="218" 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="LC201" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" 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="new_line diff-line-num old" data-linenumber="218" 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="LC202" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span></pre>

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<td class="old_line diff-line-num new" data-linenumber="203" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="218" style="width: 35px; color: rgba(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="LC218" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">open_raise_limit</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="626af34e8204774ea46e20955936146dedc828eb">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#626af34e8204774ea46e20955936146dedc828eb"><strong>tests/conftest.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,14 +10,14 @@ def cores(request):</td>

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10

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<td class="new_line diff-line-num" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

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<td class="new_line diff-line-num" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">fixture</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_run</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">inpath</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Statistics</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">            <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="17" 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="LC17" class="line" lang="python">        <span class="n" style="color: #333;">tmp_fastaq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">expected</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">        <span class="n" style="color: #333;">tmp_fastaq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">expected</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_fastaq</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="n" style="color: #333;">inpath</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python">        <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">        <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">main</span><span class="p">(<span class="idiff left">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">p</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;">params</span><span class="p"><span class="idiff right">]</span>)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO redirect standard output</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">        <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="n" style="color: #333;">expected</span><span class="p">),</span> <span class="n" style="color: #333;">tmp_fastaq</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stats</span></span>

</pre>

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</table>

<br>

</li>

<li id="5668d3b26dd09e6c19b959c5cc817ff64dc54cb6">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#5668d3b26dd09e6c19b959c5cc817ff64dc54cb6"><strong>tests/cut/info-rc.txt</strong></a>

<hr>

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</td>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">s     0       20      26      AGGCGCTTGTAGCGTCGATT    GAGTCG  TGAC    adapt                           0</span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">r     0       20      26      AGGCGCTTGTAGCGTCGATT    GAGTCG  TGAC    adapt                           1</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="5fc94fc2534bb535bfd7015f641462099d4972fa">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#5fc94fc2534bb535bfd7015f641462099d4972fa"><strong>tests/data/info-rc.fasta</strong></a>

<hr>

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</td>

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>s</span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>r</span>

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

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<br>

</li>

<li id="8b386ef32463372ea7de22d96d0771a85c1ed553">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#8b386ef32463372ea7de22d96d0771a85c1ed553"><strong>tests/test_command.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>

</pre>

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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;">sys</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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

</pre>

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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;">pytest</span></span>

</pre>

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

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

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datapath</span><span class="p">,</span> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">,</span> <span class="n" style="color: #333;">cutpath</span></span>

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<td class="new_line diff-line-num" 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>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,11 +20,12 @@ def test_run_as_module():</td>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">decode</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">()</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="LC21" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" 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="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"win32"</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Perhaps this can be fixed"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" 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="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_standard_input_pipe</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" 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="python">    <span class="s" style="color: #d14;">"""Read FASTQ from standard input"""</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">in_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">Use 'cat' to s</span>imulate that no file name is available for stdin</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># <span class="idiff left right">S</span>imulate that no file name is available for stdin</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="s" style="color: #d14;">"cat"</span><span class="p">,</span> <span class="n" style="color: #333;">in_path</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cat</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,8 +76,9 @@ def test_force_fasta_output(tmpdir, cores):</td>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fasta"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">skipif</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"win32"</span><span class="p">,</span> <span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Maybe this can be made to work"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_non_utf8_locale</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python">        <span class="p">[</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">        <span class="p">[</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">        <span class="n" style="color: #333;">env</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"LC_CTYPE"</span><span class="p">:</span> <span class="s" style="color: #d14;">"C"</span><span class="p">},</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">    <span class="p">)</span></span></pre>

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<br>

</li>

<li id="83ff0d8e113228f36b352922cbbb938d0aa9384b">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#83ff0d8e113228f36b352922cbbb938d0aa9384b"><strong>tests/test_commandline.py</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span><span class="p">,</span> <span class="n" style="color: #333;">BytesIO</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>

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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;">dnaio</span></span>

</pre>

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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;">pytest</span></span>

</pre>

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

</pre>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.__main__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="81" style="width: 35px; color: rgba(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="84" style="width: 35px; color: rgba(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">@@ -81,15 +84,15 @@ def test_lowercase(run):</td>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-a ttagacatatctccgtcg'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lowercase.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="87" 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="LC84" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rest</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rest</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="88" style="width: 35px; color: rgba(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="LC88" class="line" lang="python">    <span class="s" style="color: #d14;">"""-r/--rest-file"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python">    <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"rest.tmp"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(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="LC89" class="line" lang="python">    <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"rest.tmp"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">'--cores'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ADAPTER'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-N'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">rest</span><span class="p">],</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'rest.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">rest</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="89" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="92" style="width: 35px; color: rgba(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="LC92" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="90" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="91" 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="new_line diff-line-num old" data-linenumber="94" 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="LC91" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_restfront</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="94" 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="LC92" class="line" lang="python">    <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"rest.txt"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="94" style="width: 35px; color: rgba(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="LC94" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_restfront</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="95" style="width: 35px; color: rgba(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="LC95" class="line" lang="python">    <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"rest.txt"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ADAPTER'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-N'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-r'</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">],</span> <span class="s" style="color: #d14;">"restfront.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest.fa"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'restfront.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="114" style="width: 35px; color: rgba(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">@@ -111,12 +114,13 @@ def test_extensiontxtgz(run):</td>

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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(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="LC114" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(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="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_minimum_length</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">    <span class="s" style="color: #d14;">"""-m/--minimum-length"""</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="114" 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="new_line diff-line-num old" data-linenumber="117" 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="LC114" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-m 5 -a TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"minlen.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths.fa"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(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="LC117" class="line" lang="python">    <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-m 5 -a TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"minlen.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths.fa"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="115" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(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="LC118" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">45</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(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="LC119" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="117" 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="LC117" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_too_short</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python">    <span class="s" style="color: #d14;">"""--too-short-output"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python">    <span class="n" style="color: #333;">too_short_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'tooshort.fa'</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(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="LC122" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_too_short</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="123" style="width: 35px; color: rgba(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="LC123" class="line" lang="python">    <span class="n" style="color: #333;">too_short_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">'tooshort.fa'</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="124" style="width: 35px; color: rgba(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="LC124" class="line" lang="python">    <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">([</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(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="LC125" class="line" lang="python">        <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="python">        <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(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="131" style="width: 35px; color: rgba(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">@@ -127,14 +131,26 @@ def test_too_short(run, tmpdir, cores):</td>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_short</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>

</pre>

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

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"redirect"</span><span class="p">,</span> <span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_too_short_statistics</span><span class="p">(</span><span class="n" style="color: #333;">redirect</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(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="LC136" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"24"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

137

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

<pre style="margin: 0;">+<span id="LC137" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">redirect</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

138

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

<pre style="margin: 0;">+<span id="LC138" class="line" lang="python">        <span class="n" style="color: #333;">args</span><span class="p">[:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"--too-short-output"</span><span class="p">,</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

139

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

<pre style="margin: 0;">+<span id="LC139" class="line" lang="python">    <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

140

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

<pre style="margin: 0;">+<span id="LC140" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">with_adapters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

141

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

<pre style="margin: 0;">+<span id="LC141" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

142

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

<pre style="margin: 0;">+<span id="LC142" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">58</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

143

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

<pre style="margin: 0;">+<span id="LC143" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_short</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

144

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

<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="130" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

145

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

<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

130

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<td class="new_line diff-line-num" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

146

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_maximum_length</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

131

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<td class="new_line diff-line-num" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

147

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

<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">    <span class="s" style="color: #d14;">"""-M/--maximum-length"""</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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

148

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

<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-M 5 -a TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxlen.fa"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths.fa"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

133

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

149

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

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

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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

150

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

<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"></span>

</pre>

</td>

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

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

135

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<td class="new_line diff-line-num old" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_too_long</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="136" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

151

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

<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_too_long</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

136

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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

152

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

<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">    <span class="s" style="color: #d14;">"""--too-long-output"""</span></span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python">    <span class="n" style="color: #333;">too_long_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">'toolong.fa'</span><span class="p"><span class="idiff right">))</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="138" style="width: 35px; color: rgba(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="LC153" class="line" lang="python">    <span class="n" style="color: #333;">too_long_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'toolong.fa'</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">    <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">([</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">        <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

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<td class="new_line diff-line-num" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">        <span class="s" style="color: #d14;">"-M"</span><span class="p">,</span> <span class="s" style="color: #d14;">"5"</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" style="width: 35px; color: rgba(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="169" style="width: 35px; color: rgba(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">@@ -153,19 +169,19 @@ def test_length_tag(run):</td>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">)))</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="172" 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="LC156" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overlap_a</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overlap_a</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">):</span></span>

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<td class="new_line diff-line-num" data-linenumber="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="python">    <span class="s" style="color: #d14;">"""-O/--overlap with -a"""</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="python">    <span class="n" style="color: #333;">adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"catatctccg"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(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="LC175" class="line" lang="python">    <span class="n" style="color: #333;">record</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">">read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">GAGACCATTCCAATG"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">adapter</span><span class="p">[:</span><span class="n" style="color: #333;">length</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</span><span class="s" style="color: #d14;">'</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" 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="new_line diff-line-num old" data-linenumber="176" 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="LC160" class="line" lang="python">    <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"overlap.fasta"</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" 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="new_line diff-line-num old" data-linenumber="176" 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="LC161" class="line" lang="python">    <span class="nb" style="color: #0086b3;">input</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="176" style="width: 35px; color: rgba(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="LC176" class="line" lang="python">    <span class="nb" style="color: #0086b3;">input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"overlap.fasta"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(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="LC177" class="line" lang="python">    <span class="nb" style="color: #0086b3;">input</span><span class="p">.</span><span class="n" style="color: #333;">write<span class="idiff left right">_text</span></span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>

</pre>

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162

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<td class="new_line diff-line-num" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>

</pre>

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163

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<td class="new_line diff-line-num" data-linenumber="179" style="width: 35px; color: rgba(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="LC179" class="line" lang="python">        <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="180" style="width: 35px; color: rgba(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="LC180" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="old_line diff-line-num" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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<td class="new_line diff-line-num" data-linenumber="181" style="width: 35px; color: rgba(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="LC181" class="line" lang="python">        <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'>read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">GAGACCATTCCAATG</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>

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<td class="new_line diff-line-num old" data-linenumber="182" 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="LC166" class="line" lang="python">    <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"overlap-trimmed.fasta"</span><span class="p"><span class="idiff right">)</span></span></span>

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<td class="old_line diff-line-num new" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="182" style="width: 35px; color: rgba(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="LC182" class="line" lang="python">    <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"overlap-trimmed.fasta"</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(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="LC183" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"-O"</span><span class="p">,</span> <span class="s" style="color: #d14;">"7"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-e"</span><span class="p">,</span> <span class="s" style="color: #d14;">"0"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="168" 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="new_line diff-line-num old" data-linenumber="184" 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="LC168" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="184" style="width: 35px; color: rgba(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="LC184" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">read<span class="idiff left right">_text</span></span><span class="p">()</span></span>

</pre>

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185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="170" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_overlap_b</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="250" style="width: 35px; color: rgba(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="266" style="width: 35px; color: rgba(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">@@ -250,9 +266,9 @@ def test_read_wildcard(run):</td>

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<td class="new_line diff-line-num" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter.fa"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">"-b"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard_adapter_anywhere.fa"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="252" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="python"><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="253" 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="new_line diff-line-num old" data-linenumber="269" 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="LC253" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_wildcard</span><span class="p">(</span><span class="n" style="color: #333;">adapter_type</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_wildcard</span><span class="p">(</span><span class="n" style="color: #333;">adapter_type</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python">    <span class="s" style="color: #d14;">"""wildcards in adapter"""</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python">    <span class="n" style="color: #333;">wildcard_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"wildcards.txt"</span><span class="p"><span class="idiff right">))</span></span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python">    <span class="n" style="color: #333;">wildcard_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"wildcards.txt"</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python">            <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python">            <span class="s" style="color: #d14;">"--wildcard-file"</span><span class="p">,</span> <span class="n" style="color: #333;">wildcard_path</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -324,39 +340,52 @@ def test_ellipsis_notation(run):</td>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-a ...TTAGACATAT -g GAGATTGCCA --no-indels'</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_indels.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'no_indels.fasta'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_46</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_46</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">    <span class="s" style="color: #d14;">"""issue 46 - IndexError with --wildcard-file"""</span></span>

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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--anywhere=AACGTN --wildcard-file={}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<td class="new_line diff-line-num old" data-linenumber="346" 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="LC330" class="line" lang="python">        <span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"wildcards.txt"</span><span class="p">)<span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">"issue46.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"issue46.fasta"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python">        <span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"wildcards.txt"</span><span class="p">),</span> <span class="s" style="color: #d14;">"issue46.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"issue46.fasta"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_strip_suffix</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--strip-suffix _sequence -a XXXXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"stripped.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"simple.fasta"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="353" 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="LC337" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="338" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># The true adapter sequence in the illumina.fastq.gz data set is</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="339" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># GCCTAACTTCTTAGACTGCCTTAAGGACGT (fourth base is different from the sequence shown here)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"info.txt"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="356" style="width: 35px; color: rgba(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="LC356" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"info.txt"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="341" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(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="LC357" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTAGACTGCCTTAAGGACGT"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(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="LC358" class="line" lang="python">        <span class="s" style="color: #d14;">"illumina.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina.fastq.gz"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="343" 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="new_line diff-line-num old" data-linenumber="359" 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="LC343" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"illumina.info.txt"</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="344" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="359" style="width: 35px; color: rgba(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="LC359" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"illumina.info.txt"</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ignore_trailing_space</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="344" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="360" style="width: 35px; color: rgba(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="LC360" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="362" 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="LC346" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_times</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="347" 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="new_line diff-line-num old" data-linenumber="362" 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="LC347" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"info.txt"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="362" style="width: 35px; color: rgba(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="LC362" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_times</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="348" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="363" style="width: 35px; color: rgba(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="LC363" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"info.txt"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="348" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="364" style="width: 35px; color: rgba(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="LC364" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"--times"</span><span class="p">,</span> <span class="s" style="color: #d14;">"2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GCCGAACTTCTTA"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="349" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="365" style="width: 35px; color: rgba(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="LC365" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt2=GACTGCCTTAAGGACGT"</span><span class="p">],</span> <span class="s" style="color: #d14;">"illumina5.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina5.fastq"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="350" 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="new_line diff-line-num old" data-linenumber="366" 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="LC350" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">'illumina5.info.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="351" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="366" style="width: 35px; color: rgba(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="LC366" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">'illumina5.info.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ignore_trailing_space</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="352" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="368" style="width: 35px; color: rgba(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="LC368" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="353" 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="new_line diff-line-num old" data-linenumber="369" 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="LC353" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_fasta</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="354" 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="new_line diff-line-num old" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC354" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"info.txt"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="369" style="width: 35px; color: rgba(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="LC369" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_fasta</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="355" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="370" style="width: 35px; color: rgba(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="LC370" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"info.txt"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

355

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<td class="new_line diff-line-num" data-linenumber="371" style="width: 35px; color: rgba(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="LC371" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Just make sure that it runs</span></span>

</pre>

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356

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<td class="new_line diff-line-num" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

372

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATAT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"GAGATTGCCA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--no-indels"</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

357

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<td class="new_line diff-line-num" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

373

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

<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">        <span class="s" style="color: #d14;">"no_indels.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"no_indels.fasta"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

358

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<td class="new_line diff-line-num" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

374

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

<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

359

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<td class="new_line diff-line-num" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

375

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

<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

376

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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file_revcomp</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

377

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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"info-rc.txt"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

378

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

<pre style="margin: 0;">+<span id="LC378" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

379

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

<pre style="margin: 0;">+<span id="LC379" class="line" lang="python">        <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_path</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

380

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

<pre style="margin: 0;">+<span id="LC380" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapt=GAGTCG"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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

<pre style="margin: 0;">+<span id="LC381" class="line" lang="python">        <span class="s" style="color: #d14;">"--revcomp"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

382

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

<pre style="margin: 0;">+<span id="LC382" class="line" lang="python">        <span class="s" style="color: #d14;">"--rename={header}"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

383

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

<pre style="margin: 0;">+<span id="LC383" class="line" lang="python">        <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"out.fasta"</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

384

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

<pre style="margin: 0;">+<span id="LC384" class="line" lang="python">        <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"info-rc.fasta"</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="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

385

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

<pre style="margin: 0;">+<span id="LC385" class="line" lang="python">    <span class="p">])</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

386

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

<pre style="margin: 0;">+<span id="LC386" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"info-rc.txt"</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

387

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

<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="360" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

388

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

<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

360

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<td class="new_line diff-line-num" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

389

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

361

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<td class="new_line diff-line-num" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-a MY_ADAPTER=GCCGAACTTCTTAGACTGCCTTAAGGACGT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"illumina.fastq.gz"</span><span class="p">)</span></span>

</pre>

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391

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="439" style="width: 35px; color: rgba(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">@@ -439,11 +468,14 @@ def test_unconditional_cut_invalid_number():</td>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"-u"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a,b"</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)])</span></span>

</pre>

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440

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="python"></span>

</pre>

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441

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="471" 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="LC442" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_untrimmed_output</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC443" class="line" lang="python">    <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"untrimmed.fastq"</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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444

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<td class="new_line diff-line-num old" data-linenumber="471" 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="LC444" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--untrimmed-output"</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">],</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(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="LC471" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_untrimmed_output</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="472" style="width: 35px; color: rgba(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="LC472" class="line" lang="python">    <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"untrimmed.fastq"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="445" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="473" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

473

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<pre style="margin: 0;">+<span id="LC473" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left">stats</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--untrimmed-output"</span><span class="p">,</span> <span class="n" style="color: #333;">path</span><span class="p">],</span></span>

</pre>

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445

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<td class="new_line diff-line-num" data-linenumber="474" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

474

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python">        <span class="s" style="color: #d14;">"small.trimmed.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

446

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<td class="new_line diff-line-num" data-linenumber="475" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

475

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.untrimmed.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">path</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="447" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="476" style="width: 35px; color: rgba(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="LC476" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">with_adapters</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="477" style="width: 35px; color: rgba(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="LC477" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="478" style="width: 35px; color: rgba(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="LC478" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">46</span></span>

</pre>

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447

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<td class="new_line diff-line-num" data-linenumber="479" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

479

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="448" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

448

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<td class="new_line diff-line-num" data-linenumber="480" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

480

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

449

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<td class="new_line diff-line-num" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

481

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="560" style="width: 35px; color: rgba(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">@@ -528,7 +560,7 @@ def test_quiet_is_quiet():</td>

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<td class="old_line diff-line-num" data-linenumber="528" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

528

</td>

<td class="new_line diff-line-num" data-linenumber="560" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

560

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<pre style="margin: 0;"> <span id="LC560" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="529" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

529

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<td class="new_line diff-line-num" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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

<pre style="margin: 0;"> <span id="LC561" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">captured_standard_output</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="530" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

530

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<td class="new_line diff-line-num" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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

<pre style="margin: 0;"> <span id="LC562" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">captured_standard_error</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="531" 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">

531

</td>

<td class="new_line diff-line-num old" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC531" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">'/</span>dev<span class="idiff">/</span>null<span class="idiff right">'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

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

<td class="old_line diff-line-num new" data-linenumber="532" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="563" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

563

</td>

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

<pre style="margin: 0;">+<span id="LC563" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="532" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

532

</td>

<td class="new_line diff-line-num" data-linenumber="564" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

564

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

<pre style="margin: 0;"> <span id="LC564" class="line" lang="python">    <span class="k" style="font-weight: 600;">finally</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="533" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

533

</td>

<td class="new_line diff-line-num" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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

<pre style="margin: 0;"> <span id="LC565" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_stdout</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="534" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

534

</td>

<td class="new_line diff-line-num" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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

<pre style="margin: 0;"> <span id="LC566" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_stderr</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="539" style="width: 35px; color: rgba(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="571" style="width: 35px; color: rgba(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">@@ -539,7 +571,7 @@ def test_quiet_is_quiet():</td>

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<td class="old_line diff-line-num" data-linenumber="539" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

539

</td>

<td class="new_line diff-line-num" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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

<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="540" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

540

</td>

<td class="new_line diff-line-num" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

572

</td>

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

<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

541

</td>

<td class="new_line diff-line-num" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

573

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

<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_x_brace_notation</span><span class="p">():</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="542" 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">

542

</td>

<td class="new_line diff-line-num old" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC542" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">'/</span>dev<span class="idiff">/</span>null<span class="idiff right">'</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'X{5}'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="543" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

</td>

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

<pre style="margin: 0;">+<span id="LC574" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="s" style="color: #d14;">'--quiet'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'X{5}'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

</td>

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543

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"></span>

</pre>

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544

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<td class="new_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(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="LC576" class="line" lang="python"></span>

</pre>

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545

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<td class="new_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(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="LC577" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nextseq</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" style="width: 35px; color: rgba(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="607" style="width: 35px; color: rgba(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">@@ -575,11 +607,11 @@ def test_linked_lowercase(run):</td>

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575

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<td class="new_line diff-line-num" data-linenumber="607" style="width: 35px; color: rgba(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="LC607" class="line" lang="python">        <span class="s" style="color: #d14;">'linked-lowercase.fasta'</span><span class="p">,</span> <span class="s" style="color: #d14;">'linked.fasta'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<td class="new_line diff-line-num" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

608

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

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<td class="new_line diff-line-num" data-linenumber="609" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

609

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="578" 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">

578

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<td class="new_line diff-line-num old" data-linenumber="610" 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="LC578" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_info_file</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="579" 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">

579

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<td class="new_line diff-line-num old" data-linenumber="610" 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="LC579" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmpdir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">'info.txt'</span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="580" 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">

580

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<td class="new_line diff-line-num old" data-linenumber="610" 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="LC580" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-a linkedadapter=^AAAAAAAAAA...TTTTTTTTTT'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--info-file'</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="581" 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">

581

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<td class="new_line diff-line-num old" data-linenumber="610" 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="LC581" class="line" lang="python">        <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">'out.fasta'</span><span class="p">)<span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked.fasta'</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="582" 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">

582

</td>

<td class="new_line diff-line-num old" data-linenumber="610" 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="LC582" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked-info.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="610" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

610

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_info_file</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="611" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

611

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<pre style="margin: 0;">+<span id="LC611" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'info.txt'</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

612

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

<pre style="margin: 0;">+<span id="LC612" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-a linkedadapter=^AAAAAAAAAA...TTTTTTTTTT'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--info-file'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;">info_path</span><span class="p"><span class="idiff right">)</span>,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="613" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

613

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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python">        <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'out.fasta'</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked.fasta'</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="583" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

614

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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked-info.txt'</span><span class="p">),</span> <span class="n" style="color: #333;">info_path</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ignore_trailing_space</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="617" style="width: 35px; color: rgba(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="LC617" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_anywhere</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="614" style="width: 35px; color: rgba(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="646" style="width: 35px; color: rgba(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">@@ -614,14 +646,19 @@ def test_negative_length(run):</td>

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<td class="new_line diff-line-num" data-linenumber="646" style="width: 35px; color: rgba(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="LC646" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="647" style="width: 35px; color: rgba(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="LC647" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="648" style="width: 35px; color: rgba(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="LC648" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="617" 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">

617

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<td class="new_line diff-line-num old" data-linenumber="649" 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="LC617" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_296</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="618" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="649" style="width: 35px; color: rgba(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="LC649" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_296</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="618" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="650" style="width: 35px; color: rgba(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="LC650" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Hang when using both --no-trim and --info-file together</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="619" 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="new_line diff-line-num old" data-linenumber="651" 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="LC619" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'info.txt'</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="620" 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">

620

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<td class="new_line diff-line-num old" data-linenumber="651" 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="LC620" class="line" lang="python">    <span class="n" style="color: #333;">reads_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'reads.fasta'</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="621" 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">

621

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<td class="new_line diff-line-num old" data-linenumber="651" 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="LC621" class="line" lang="python">    <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'out.fasta'</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="622" 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">

622

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<td class="new_line diff-line-num old" data-linenumber="651" 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="LC622" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">reads_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="623" 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">

623

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<td class="new_line diff-line-num old" data-linenumber="651" 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="LC623" class="line" lang="python">        <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">'>read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CACAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="624" 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">

624

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<td class="new_line diff-line-num old" data-linenumber="651" 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="LC624" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--info-file'</span><span class="p">,</span> <span class="n" style="color: #333;">info_path</span><span class="p">,</span> <span class="s" style="color: #d14;">'--no-trim'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-g'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TTTCAC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="n" style="color: #333;">reads_path</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

651

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<pre style="margin: 0;">+<span id="LC651" class="line" lang="python">    <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">'info.txt'</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="625" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="652" style="width: 35px; color: rgba(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="LC652" class="line" lang="python">    <span class="n" style="color: #333;">reads_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">'reads.fasta'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python">    <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">'out.fasta'</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(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="LC654" class="line" lang="python">    <span class="n" style="color: #333;">reads_path</span><span class="p">.</span><span class="n" style="color: #333;">write_text</span><span class="p">(</span><span class="s" style="color: #d14;">">read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">CACAAA</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC655" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="656" style="width: 35px; color: rgba(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="LC656" class="line" lang="python">        <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">info_path</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC657" class="line" lang="python">        <span class="s" style="color: #d14;">"--no-trim"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC658" class="line" lang="python">        <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTCAC"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC659" class="line" lang="python">        <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python">        <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">reads_path</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python">    <span class="p">])</span></span>

</pre>

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625

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Output should be unchanged because of --no-trim</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python">    <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">reads_path</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="664" style="width: 35px; color: rgba(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="LC664" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="649" style="width: 35px; color: rgba(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="686" style="width: 35px; color: rgba(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">@@ -649,8 +686,8 @@ def test_cores_autodetect(run):</td>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'--cores 0 -b TTAGACATATCTCCGTCG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'underscore_fastq.gz'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_write_compressed_fastq</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--cores'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">'out.fastq.gz'</span><span class="p">)<span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

689

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_write_compressed_fastq</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="654" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

690

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'--cores'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">'-o'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">'out.fastq.gz'</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

654

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<td class="new_line diff-line-num" data-linenumber="691" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

691

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

<pre style="margin: 0;"> <span id="LC691" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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<td class="new_line diff-line-num" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

692

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<td class="new_line diff-line-num" data-linenumber="693" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

693

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_minimal_report</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="667" style="width: 35px; color: rgba(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="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -667,9 +704,9 @@ def test_empty_read_with_wildcard_in_adapter(run):</td>

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<td class="old_line diff-line-num" data-linenumber="667" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

667

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<td class="new_line diff-line-num" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-g CWC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"empty.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"empty.fastq"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="668" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

668

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<td class="new_line diff-line-num" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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

<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="669" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

669

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

<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="670" 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">

670

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<td class="new_line diff-line-num old" data-linenumber="707" 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="LC670" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_print_progress_to_tty</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">dir</span></span><span class="p">,</span> <span class="n" style="color: #333;">mocker</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="671" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

707

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

<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_print_progress_to_tty</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left right">_path</span></span><span class="p">,</span> <span class="n" style="color: #333;">mocker</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="671" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

671

</td>

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

<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">    <span class="n" style="color: #333;">mocker</span><span class="p">.</span><span class="n" style="color: #333;">patch</span><span class="p">(</span><span class="s" style="color: #d14;">"cutadapt.utils.sys.stderr"</span><span class="p">).</span><span class="n" style="color: #333;">isatty</span><span class="p">.</span><span class="n" style="color: #333;">return_value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="672" 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">

672

</td>

<td class="new_line diff-line-num old" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC672" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">dir</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)<span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="673" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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">

709

</td>

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

<pre style="margin: 0;">+<span id="LC709" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp<span class="idiff left">_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff right"> </span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

673

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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

674

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<td class="new_line diff-line-num" 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" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="675" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

675

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712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_adapter_order</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="677" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -677,6 +714,24 @@ def test_adapter_order(run):</td>

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<td class="old_line diff-line-num" data-linenumber="677" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

677

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">    <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-a CCGGG -g ^AAACC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapterorder-ag.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapterorder.fasta"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="678" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

678

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="679" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

679

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<td class="new_line diff-line-num" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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

<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" 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">

717

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

<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_complement_no_rc_suffix</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

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

<pre style="margin: 0;">+<span id="LC718" class="line" lang="python">    <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"out.fastq"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

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

<pre style="margin: 0;">+<span id="LC719" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

720

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

<pre style="margin: 0;">+<span id="LC720" class="line" lang="python">        <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">),</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

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

<pre style="margin: 0;">+<span id="LC721" class="line" lang="python">        <span class="s" style="color: #d14;">"--revcomp"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

722

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

<pre style="margin: 0;">+<span id="LC722" class="line" lang="python">        <span class="s" style="color: #d14;">"--no-index"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

</td>

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

<pre style="margin: 0;">+<span id="LC723" class="line" lang="python">        <span class="s" style="color: #d14;">"--rename"</span><span class="p">,</span> <span class="s" style="color: #d14;">"{header}"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

724

</td>

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

<pre style="margin: 0;">+<span id="LC724" class="line" lang="python">        <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"^TTATTTGTCT"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

725

</td>

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

<pre style="margin: 0;">+<span id="LC725" class="line" lang="python">        <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span> <span class="s" style="color: #d14;">"^TCCGCACTGG"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

726

</td>

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

<pre style="margin: 0;">+<span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"revcomp.1.fastq"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

727

</td>

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

<pre style="margin: 0;">+<span id="LC727" class="line" lang="python">    <span class="p">])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

728

</td>

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

<pre style="margin: 0;">+<span id="LC728" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">dnaio</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

729

</td>

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

<pre style="margin: 0;">+<span id="LC729" class="line" lang="python">        <span class="n" style="color: #333;">reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

730

</td>

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

<pre style="margin: 0;">+<span id="LC730" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

731

</td>

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<pre style="margin: 0;">+<span id="LC731" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"read2/1"</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

732

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

<pre style="margin: 0;">+<span id="LC732" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">reads</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"ACCATCCGATATGTCTAATGTGGCCTGTTG"</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

733

</td>

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

<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="680" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

734

</td>

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

<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="680" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

680

</td>

<td class="new_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

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<pre style="margin: 0;"> <span id="LC735" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_complement_normalized</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="681" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

681

</td>

<td class="new_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python">    <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="682" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

682

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<td class="new_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

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<pre style="margin: 0;"> <span id="LC737" class="line" lang="python">        <span class="s" style="color: #d14;">"--revcomp --no-index -g ^TTATTTGTCT -g ^TCCGCACTGG"</span><span class="p">,</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="773" style="width: 35px; color: rgba(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">@@ -718,12 +773,12 @@ def test_max_expected_errors(run, cores):</td>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_max_expected_errors_fasta</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

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

<pre style="margin: 0;"> <span id="LC774" class="line" lang="python">    <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"input.fasta"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<td class="new_line diff-line-num" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

775

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<pre style="margin: 0;"> <span id="LC775" class="line" lang="python">    <span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">write_text</span><span class="p">(</span><span class="s" style="color: #d14;">">read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACGTACGT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="721" 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">

721

</td>

<td class="new_line diff-line-num old" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC721" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--max-ee=0.001"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="722" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

776

</td>

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

<pre style="margin: 0;">+<span id="LC776" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--max-ee=0.001"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

</td>

<td class="new_line diff-line-num" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

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

<pre style="margin: 0;"> <span id="LC777" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

</td>

<td class="new_line diff-line-num" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

</td>

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

<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

<td class="new_line diff-line-num" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

</td>

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

<pre style="margin: 0;"> <span id="LC779" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_warn_if_en_dashes_used</span><span class="p">():</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="new_line diff-line-num" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

</td>

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

<pre style="margin: 0;"> <span id="LC780" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="726" 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">

726

</td>

<td class="new_line diff-line-num old" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"–q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"25"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"in.fastq"</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="727" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

781

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

<pre style="margin: 0;">+<span id="LC781" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"–q"</span><span class="p">,</span> <span class="s" style="color: #d14;">"25"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="s" style="color: #d14;">"in.fastq"</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

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<td class="new_line diff-line-num" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="new_line diff-line-num" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="729" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

729

</td>

<td class="new_line diff-line-num" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

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

<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"opt"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"-y"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--suffix"</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="735" style="width: 35px; color: rgba(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="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -735,7 +790,7 @@ def test_suffix(opt, run):</td>

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<td class="old_line diff-line-num" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

</td>

<td class="new_line diff-line-num" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"opt"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"--prefix"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--suffix"</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="new_line diff-line-num" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rename_cannot_be_combined_with_other_renaming_options</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

<td class="new_line diff-line-num" data-linenumber="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

792

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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="738" 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">

738

</td>

<td class="new_line diff-line-num old" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC738" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="s" style="color: #d14;">"something"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--rename='{id} {comment} extrainfo'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"empty.fastq"</span><span class="p">)])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="739" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

793

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<pre style="margin: 0;">+<span id="LC793" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="s" style="color: #d14;">"something"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--rename='{id} {comment} extrainfo'"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"empty.fastq"</span><span class="p">)])</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

<td class="new_line diff-line-num" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

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

<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

<td class="new_line diff-line-num" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

</td>

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

<pre style="margin: 0;"> <span id="LC795" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

<td class="new_line diff-line-num" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rename</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>

</pre>

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<br>

</li>

<li id="124a8b77d32c7ca9f7f1966a0cde3894ce860e05">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#124a8b77d32c7ca9f7f1966a0cde3894ce860e05"><strong>tests/test_main.py</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,5 +42,5 @@ def test_parse_lengths():</td>

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42

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

42

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_setup_logging</span><span class="p">():</span></span>

</pre>

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

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="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="old_line diff-line-num" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">    <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python">    <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">stdout</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Tru</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">    <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">log_to_stderr</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">Fals</span>e</span><span class="p">,</span> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">    <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Log message"</span><span class="p">)</span></span></pre>

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<br>

</li>

<li id="aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda"><strong>tests/test_modifiers.py</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -206,6 +206,16 @@ class TestRenamer:</td>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">        <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">cut_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"TTAAGG"</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">renamer</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"theid_TTAAGG thecomment"</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_rc_template_varialbe</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python">        <span class="n" style="color: #333;">renamer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Renamer</span><span class="p">(</span><span class="s" style="color: #d14;">"{id} rc={rc} {comment}"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="211" style="width: 35px; color: rgba(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="LC211" class="line" lang="python">        <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"theid thecomment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="212" style="width: 35px; color: rgba(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="LC212" class="line" lang="python">        <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="213" style="width: 35px; color: rgba(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="LC213" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">renamer</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"theid rc= thecomment"</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="214" style="width: 35px; color: rgba(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="LC214" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python">        <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"theid thecomment"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="216" style="width: 35px; color: rgba(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="LC216" class="line" lang="python">        <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">is_rc</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">renamer</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">).</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"theid rc=rc thecomment"</span></span>

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>

</pre>

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209

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestPairedEndRenamer</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid_template_variable</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<br>

</li>

<li id="4ad7124461a591ee5c5c2e30f24380a477c3ed52">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#4ad7124461a591ee5c5c2e30f24380a477c3ed52"><strong>tests/test_paired.py</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>

</pre>

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">shutil</span></span>

</pre>

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3

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4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">product</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="121" style="width: 35px; color: rgba(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="122" style="width: 35px; color: rgba(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">@@ -121,14 +122,14 @@ def test_explicit_format_with_paired(tmpdir, run_paired):</td>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_trimming_legacy</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># make sure that this doesn"t divide by zero</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="124" 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="new_line diff-line-num old" data-linenumber="125" 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="LC124" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="125" style="width: 35px; color: rgba(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="LC125" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="125" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="126" style="width: 35px; color: rgba(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="LC126" class="line" lang="python">        <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)])</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_trimming</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># make sure that this doesn"t divide by zero</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

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<td class="old_line diff-line-num old" data-linenumber="131" 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="new_line diff-line-num old" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff">"</span></span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">        <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"XXXXX"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="133" style="width: 35px; color: rgba(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="LC133" class="line" lang="python">        <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)])</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

134

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -147,7 +148,7 @@ def test_first_too_short(tmpdir, cores):</td>

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

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="150" 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="new_line diff-line-num old" data-linenumber="151" 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="LC150" class="line" lang="python">            <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(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="LC151" class="line" lang="python">            <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="python">            <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="152" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="python">            <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="153" style="width: 35px; color: rgba(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="new_line diff-line-num" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">            <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc1</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="164" style="width: 35px; color: rgba(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="165" style="width: 35px; color: rgba(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">@@ -164,7 +165,7 @@ def test_second_too_short(tmpdir, cores):</td>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">([</span></span>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python">            <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;"><span class="idiff left">"/</span>dev<span class="idiff">/</span>null<span class="idiff right">"</span></span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python">            <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff right">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python">            <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">            <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>

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<td class="new_line diff-line-num" data-linenumber="171" style="width: 35px; color: rgba(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="LC171" class="line" lang="python">            <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc2</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,7 +193,7 @@ def test_unmatched_read_names(tmpdir, cores):</td>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_p_without_o</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python">    <span class="s" style="color: #d14;">"""Option -p given but -o missing"""</span></span>

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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

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<td class="new_line diff-line-num old" data-linenumber="196" 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="LC195" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="s" style="color: #d14;">"-a<span class="idiff left"> XX -p /</span>dev<span class="idiff">/</span>null<span class="idiff">"</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff right">()</span></span></span>

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<td class="new_line diff-line-num new" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">(<span class="idiff left">[</span></span><span class="s" style="color: #d14;">"-a<span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"XX"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-p"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p"><span class="idiff right">]</span></span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(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="LC197" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">)]</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(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="LC198" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)])</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(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="LC199" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="200" style="width: 35px; color: rgba(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="201" style="width: 35px; color: rgba(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">@@ -200,7 +201,7 @@ def test_p_without_o(cores):</td>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_paired_but_only_one_input_file</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">    <span class="s" style="color: #d14;">"""Option -p given but only one input file"""</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="s" style="color: #d14;">"-a<span class="idiff left"> XX -o /</span>dev<span class="idiff">/</span>null<span class="idiff"> -p /</span>dev<span class="idiff">/</span>null<span class="idiff">"</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff right">()</span></span></span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python">        <span class="n" style="color: #333;">main</span><span class="p">(<span class="idiff left">[</span></span><span class="s" style="color: #d14;">"-a<span class="idiff">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"XX"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-o"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"-p"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;">devnull</span><span class="p"><span class="idiff right">]</span></span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">)])</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>

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<br>

</li>

<li id="9627b71ff9952493fda5865aea912319edd1cdd2">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#9627b71ff9952493fda5865aea912319edd1cdd2"><strong>tests/test_parser.py</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,6 +66,15 @@ def test_parse_not_linked():</td>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'a_name=ADAPT'</span><span class="p">,</span> <span class="s" style="color: #d14;">'front'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="p">(</span><span class="s" style="color: #d14;">'a_name'</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'ADAPT'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'front'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(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="LC69" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"where"</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">"front"</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(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="LC70" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"reqopt"</span><span class="p">,</span> <span class="p">(</span><span class="s" style="color: #d14;">"required"</span><span class="p">,</span> <span class="s" style="color: #d14;">"optional"</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_invalid_adapter_specific_parameter</span><span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">,</span> <span class="n" style="color: #333;">reqopt</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(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="LC72" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">        <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">_parse_not_linked</span><span class="p">(</span><span class="s" style="color: #d14;">"A;{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">reqopt</span><span class="p">),</span> <span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"can only be used within linked adapters"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_invalid_cmdline_type</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="80" style="width: 35px; color: rgba(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="LC80" class="line" lang="python">        <span class="n" style="color: #333;">AdapterSpecification</span><span class="p">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'invalid_type'</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="570726290219a04b926b9aa2c02fe1ba4204124a">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#570726290219a04b926b9aa2c02fe1ba4204124a"><strong>tests/utils.py</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>

</pre>

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<td class="new_line diff-line-num" 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="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,9 +15,18 @@ class FilesDifferent(Exception):</td>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">    <span class="k" style="font-weight: 600;">pass</span></span>

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

</pre>

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

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<td class="old_line diff-line-num old" data-linenumber="17" 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="new_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_trailing_space</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"diff"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-u"</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="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"win32"</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="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"--strip-trailing-cr"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

22

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ignore_trailing_space</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="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">platform</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"darwin"</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="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Ignores too much, but macOS doesn’t have the option below</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">            <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"-b"</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="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

26

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">            <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"--ignore-trailing-space"</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" 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

</td>

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

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

19

</td>

<td class="new_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">        <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(<span class="idiff left">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'diff'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'-u'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">],</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">STDOUT</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="old_line diff-line-num new" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

29

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">        <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">cmd</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[</span></span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">path2</span><span class="p">],</span> <span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">STDOUT</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

<td class="new_line diff-line-num" 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">

30

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">CalledProcessError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">FilesDifferent</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">.</span><span class="n" style="color: #333;">decode</span><span class="p">())</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="old_line diff-line-num" 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">

22

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<td class="new_line diff-line-num" 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">

32

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

<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">

<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/a93b33f441d39ebc55c7c5a4de421ba368c63be1#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</strong></a>

<hr>

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

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

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,7 +16,7 @@ commands =</td>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="ini">    <span class="err" style="color: #a61717; background-color: #e3d2d2;">coverage</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">xml</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC17" class="line" lang="ini"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:docs]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" 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="new_line diff-line-num old" data-linenumber="19" 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="LC19" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">6</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">7</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="ini"><span class="py">changedir</span> <span class="p">=</span> <span class="s" style="color: #d14;">doc</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC21" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="ini">    <span class="err" style="color: #a61717; background-color: #e3d2d2;">sphinx</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,13 +24,13 @@ deps =</td>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span> <span class="s" style="color: #d14;">sphinx-build -W -b html -d {envtmpdir}/doctrees . {envtmpdir}/html</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="ini"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:flake8]</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="27" 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="LC27" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">6</span></span></span>

</pre>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" data-linenumber="27" style="width: 35px; color: rgba(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="LC27" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">7</span></span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="ini"><span class="py">skip_install</span> <span class="p">=</span> <span class="s" style="color: #d14;">true</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC30" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span> <span class="s" style="color: #d14;">flake8 src/ tests/</span></span>

</pre>

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<td class="old_line diff-line-num" 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="ini"></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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="ini"><span class="nn" style="color: #555;">[testenv:mypy]</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" 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="new_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC33" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">6</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(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="new_line diff-line-num new" data-linenumber="33" style="width: 35px; color: rgba(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="LC33" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.<span class="idiff left right">7</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

34

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<td class="new_line diff-line-num" data-linenumber="34" style="width: 35px; color: rgba(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="LC34" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span> <span class="s" style="color: #d14;">mypy</span></span>

</pre>

</td>

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35

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35

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span> <span class="s" style="color: #d14;">mypy src/</span></span>

</pre>

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36

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36

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

<pre style="margin: 0;"> <span id="LC36" class="line" lang="ini"></span>

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