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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cutadapt">Debian Med / python-cutadapt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc">ba3c2a62</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-10-26T15:52:07Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5</pre>
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<h4>22 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">
CHANGES.rst
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</li>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#0b1eedd0343560cd8bfa05d02964a97119a48517">
doc/algorithms.rst
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<li class="file-stats">
<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">
doc/guide.rst
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<li class="file-stats">
<a href="#424bdd8abf4cafd01bc7dcc71a6f82953c965ed0">
doc/ideas.rst
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<li class="file-stats">
<a href="#6677207c6fa30ac9cec19ad036ae842582159ecb">
doc/installation.rst
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<li class="file-stats">
<a href="#babdfe5d368a4907abadce7f9b00dfab2489185a">
src/cutadapt/__main__.py
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<li class="file-stats">
<a href="#3fdf9aa7a8f7f494997913e3e527a05e6d95fa34">
src/cutadapt/_align.c
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<li class="file-stats">
<a href="#4045e163dd270b4b21bcebce419a3b9ab8ffb64e">
src/cutadapt/_version.py
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<li class="file-stats">
<a href="#8fb347891ec0a40b16ef2bdbe361f823e12aa016">
src/cutadapt/adapters.py
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<a href="#6ed465db6839a69141086c2acf1dc01a8b17a981">
src/cutadapt/filters.py
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<a href="#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae">
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+
src/cutadapt/log.py
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<li class="file-stats">
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src/cutadapt/parser.py
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<li class="file-stats">
<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">
src/cutadapt/pipeline.py
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<li class="file-stats">
<a href="#9ba37233f76e56f10585b4e480e28b5cc079a733">
src/cutadapt/qualtrim.c
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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="#4c91f80a781e5621e92c74fdd1bddaa8ef6b43e7">
tests/test_adapters.py
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<li class="file-stats">
<a href="#83ff0d8e113228f36b352922cbbb938d0aa9384b">
tests/test_commandline.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">
<span class="new-file">
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tests/test_parser.py
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<h4>Changes:</h4>
<li id="4990be809a537bf86e4be2fe2e8251c83d8bd129">
<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#4990be809a537bf86e4be2fe2e8251c83d8bd129"><strong>CHANGES.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,22 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Changes</span></span>
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"><span class="p">=======</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"></span>
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5
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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="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">v2</span><span class="m" style="color: #099;">.5</span> <span class="p">(</span><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">09</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="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="p">-----------------</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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="mosel"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">391</span><span class="p">`:</span> <span class="n" style="color: #333;">Multicore</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">supported</span> <span class="n" style="color: #333;">even</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">using</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="p">``--</span><span class="n" style="color: #333;">untrimmed</span><span class="p">-</span><span class="n" style="color: #333;">output</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">too</span><span class="p">-</span><span class="n" style="color: #333;">short</span><span class="p">-</span><span class="n" style="color: #333;">output</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">too</span><span class="p">-</span><span class="n" style="color: #333;">long</span><span class="p">-</span><span class="n" style="color: #333;">output</span><span class="p">``</span></span>
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<td class="diff-line-num new old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">corresponding</span> <span class="p">``...-</span><span class="n" style="color: #333;">paired</span><span class="p">-</span><span class="n" style="color: #333;">output</span><span class="p">``</span> <span class="k" style="font-weight: 600;">options</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">393</span><span class="p">`:</span> <span class="n" style="color: #333;">Using</span> <span class="p">``--</span><span class="n" style="color: #333;">info</span><span class="p">-</span><span class="n" style="color: #333;">file</span><span class="p">``</span> <span class="n" style="color: #333;">no</span> <span class="n" style="color: #333;">longer</span> <span class="n" style="color: #333;">crashes</span> <span class="n" style="color: #333;">when</span> <span class="n" style="color: #333;">processing</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">paired</span><span class="p">-</span><span class="k" style="font-weight: 600;">end</span> <span class="n" style="color: #333;">data</span><span class="p">.</span> <span class="n" style="color: #333;">However</span><span class="p">,</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;">itself</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">contain</span> <span class="n" style="color: #333;">results</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">R1</span><span class="p">.</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">394</span><span class="p">`:</span> <span class="k" style="font-weight: 600;">Options</span> <span class="p">``-</span><span class="n" style="color: #333;">e</span><span class="p">``/``--</span><span class="n" style="color: #333;">no</span><span class="p">-</span><span class="n" style="color: #333;">indels</span><span class="p">``/``-</span><span class="n" style="color: #333;">O</span><span class="p">``</span> <span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">ignored</span> <span class="n" style="color: #333;">for</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> <span class="n" style="color: #333;">linked</span> <span class="n" style="color: #333;">adapters</span></span>
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<pre style="margin: 0;">+<span id="LC16" 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;">When</span> <span class="n" style="color: #333;">a</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">“</span><span class="n" style="color: #333;">Too</span> <span class="n" style="color: #333;">many</span> <span class="n" style="color: #333;">open</span> <span class="n" style="color: #333;">files</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">”</span> <span class="n" style="color: #333;">error</span> <span class="n" style="color: #333;">occurs</span> <span class="n" style="color: #333;">during</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">demultiplexing</span><span class="p">,</span> <span class="n" style="color: #333;">Cutadapt</span> <span class="n" style="color: #333;">can</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">automatically</span> <span class="n" style="color: #333;">raise</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limit</span> <span class="k" style="font-weight: 600;">and</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"> <span class="n" style="color: #333;">re</span><span class="p">-</span><span class="n" style="color: #333;">try</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">limit</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">“</span><span class="n" style="color: #333;">soft</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">”</span> <span class="n" style="color: #333;">limit</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="mosel"><span class="n" style="color: #333;">v2</span><span class="m" style="color: #099;">.4</span> <span class="p">(</span><span class="m" style="color: #099;">2019</span><span class="p">-</span><span class="m" style="color: #099;">07</span><span class="p">-</span><span class="m" style="color: #099;">09</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="mosel"><span class="p">-----------------</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 2.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: cutadapt</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 2.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 2.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: trim adapters from high-throughput sequencing reads</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: https://cutadapt.readthedocs.io/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Marcel Martin</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,9 +8,15 @@ Author-email: marcel.martin@scilifelab.se</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">License: MIT</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">Description: .. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> :target: https://travis-ci.org/marcelm/cutadapt</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> :alt:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> .. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> :target: https://pypi.python.org/pypi/cutadapt</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> .. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> :target: https://codecov.io/gh/marcelm/cutadapt</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> ========</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> Cutadapt</span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.. image:: https://travis-ci.org/marcelm/cutadapt.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> :target: https://travis-ci.org/marcelm/cutadapt</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.. image:: https://img.shields.io/pypi/v/cutadapt.svg?branch=master</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> :target: https://pypi.python.org/pypi/cutadapt</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.. image:: https://codecov.io/gh/marcelm/cutadapt/branch/master/graph/badge.svg</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> :target: https://codecov.io/gh/marcelm/cutadapt</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> :alt:</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">========</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Cutadapt</span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#0b1eedd0343560cd8bfa05d02964a97119a48517"><strong>doc/algorithms.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,7 +73,7 @@ overlaps that are actually allowed by the adapter type are actually considered.</td>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext">.. _quality-trimming-algorithm:</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext">Quality trimming algorithm</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="plaintext"><span class="idiff left right">--------------------------</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"><span class="idiff left right">==========================</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">The trimming algorithm implemented in Cutadapt is the same as the one used by</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">BWA, but applied to both</span>
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<li id="ee1d7278a009e2c5c652622fe43dc77e39af740d">
<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,9 +149,6 @@ There are some limitations at the moment:</td>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="plaintext"> - ``--info-file``</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"> - ``--rest-file``</span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext"> - ``--wildcard-file``</span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="plaintext"> - ``--untrimmed-output``, ``--untrimmed-paired-output``</span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="plaintext"> - ``--too-short-output``, ``--too-short-paired-output``</span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="plaintext"> - ``--too-long-output``, ``--too-long-paired-output``</span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">* Multi-core is also not compatible with ``--format``</span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"></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">@@ -167,6 +164,10 @@ Some of these limitations will be lifted in the future, as time allows.</td>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext">.. versionadded:: 1.18</span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"> ``--cores=0`` for autodetection</span>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">.. versionadded:: 2.5</span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> Multicore works with ``--untrimmed/too-short/too-long-(paired)-output``</span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext">Speed-up tricks</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext">---------------</span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"></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">@@ -927,23 +928,29 @@ Quality trimming</td>
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<pre style="margin: 0;"> <span id="LC928" class="line" lang="plaintext">----------------</span>
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<pre style="margin: 0;"> <span id="LC929" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC930" class="line" lang="plaintext">The ``-q`` (or ``--quality-cutoff``) parameter can be used to trim</span>
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<pre style="margin: 0;">-<span id="LC930" class="line" lang="plaintext">low-quality ends from reads before adapter removal. For this to work</span>
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<pre style="margin: 0;">-<span id="LC931" class="line" lang="plaintext">correctly, the quality values must be encoded as ascii(phred quality +</span>
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<pre style="margin: 0;">-<span id="LC932" class="line" lang="plaintext">33). If they are encoded as ascii(phred quality + 64), you need to add</span>
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<pre style="margin: 0;">-<span id="LC933" class="line" lang="plaintext">``--quality-base=64`` to the command line.</span>
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<pre style="margin: 0;">-<span id="LC934" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC935" class="line" lang="plaintext">Quality trimming can be done without adapter trimming, so this will work::</span>
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="plaintext">low-quality ends from reads. If you specify a single cutoff value, the</span>
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="plaintext">3' end of each read is trimmed::</span>
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC934" class="line" lang="plaintext"> cutadapt -q 10 -o output.fastq input.fastq</span>
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<pre style="margin: 0;"> <span id="LC935" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC939" class="line" lang="plaintext">By default, only the 3' end of each read is quality-trimmed. If you want to</span>
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<pre style="margin: 0;">-<span id="LC940" class="line" lang="plaintext">trim the 5' end as well, use the ``-q`` option with two comma-separated cutoffs::</span>
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext">For Illumina reads, this is sufficient as their quality is high at the beginning,</span>
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext">but degrades towards the 3' end.</span>
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext">It is also possible to also trim from the 5' end by specifying two</span>
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext">comma-separated cutoffs as *5' cutoff,3' cutoff*. For example, ::</span>
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<pre style="margin: 0;"> <span id="LC941" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC942" class="line" lang="plaintext"> cutadapt -q 15,10 -o output.fastq input.fastq</span>
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<pre style="margin: 0;"> <span id="LC943" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC944" class="line" lang="plaintext">The 5' end will then be trimmed with a cutoff of 15, and the 3' end will be</span>
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<pre style="margin: 0;">-<span id="LC945" class="line" lang="plaintext">trimmed with a cutoff of 10. If you only want to trim the 5' end, then use a</span>
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<pre style="margin: 0;">-<span id="LC946" class="line" lang="plaintext">cutoff of 0 for the 3' end, as in ``-q 10,0``.</span>
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext">will quality-trim the 5' end with a cutoff of 15 and the 3' end with a cutoff</span>
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext">of 10. To only trim the 5' end, use a cutoff of 0 for the 3' end, as in</span>
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext">``-q 15,0``.</span>
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<pre style="margin: 0;">+<span id="LC947" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC948" class="line" lang="plaintext">Quality trimming is done before any adapter trimming.</span>
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<pre style="margin: 0;">+<span id="LC949" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC950" class="line" lang="plaintext">By default, quality values are assumed to be encoded as</span>
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<pre style="margin: 0;">+<span id="LC951" class="line" lang="plaintext">ascii(phred quality + 33). Nowadays, this should always be the case.</span>
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<pre style="margin: 0;">+<span id="LC952" class="line" lang="plaintext">Some old Illumina FASTQ files encode qualities as ascii(phred quality + 64).</span>
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<pre style="margin: 0;">+<span id="LC953" class="line" lang="plaintext">For those, you must add ``--quality-base=64`` to the command line.</span>
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<pre style="margin: 0;"> <span id="LC954" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC955" class="line" lang="plaintext">A :ref:`description of the quality-trimming algorithm is also</span>
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<pre style="margin: 0;"> <span id="LC956" class="line" lang="plaintext">available <quality-trimming-algorithm>`. The algorithm is the same as used by BWA.</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">@@ -955,11 +962,11 @@ Quality trimming of reads using two-color chemistry (NextSeq)</td>
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<pre style="margin: 0;"> <span id="LC962" class="line" lang="plaintext">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</span>
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963
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<pre style="margin: 0;"> <span id="LC963" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC964" class="line" lang="plaintext">Some Illumina instruments use a two-color chemistry to encode the four bases.</span>
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958
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<pre style="margin: 0;">-<span id="LC958" class="line" lang="plaintext">This includes the NextSeq and the <span class="idiff left right">(at the time of this writing) recently</span></span>
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<pre style="margin: 0;">-<span id="LC959" class="line" lang="plaintext"><span class="idiff left right">announced NovaSeq. In those instruments, a </span>'dark cycle' (with no detected color)</span>
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965
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<pre style="margin: 0;">+<span id="LC965" class="line" lang="plaintext">This includes the NextSeq and the <span class="idiff left right">NovaSeq. In those instruments, a</span></span>
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<pre style="margin: 0;">+<span id="LC966" class="line" lang="plaintext">'dark cycle' (with no detected color)</span>
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960
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<pre style="margin: 0;"> <span id="LC967" class="line" lang="plaintext">encodes a ``G``. However, dark cycles also occur when when sequencing "falls</span>
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961
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968
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<pre style="margin: 0;"> <span id="LC968" class="line" lang="plaintext">off" the end of the fragment. The read then `contains a run of high-quality, but</span>
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<pre style="margin: 0;">-<span id="LC962" class="line" lang="plaintext">incorrect <span class="idiff left right">``G``</span> calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_</span>
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<pre style="margin: 0;">+<span id="LC969" class="line" lang="plaintext">incorrect <span class="idiff left right">“G”</span> calls <https://sequencing.qcfail.com/articles/illumina-2-colour-chemistry-can-overcall-high-confidence-g-bases/>`_</span>
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="plaintext">at its 3' end.</span>
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC972" class="line" lang="plaintext">Since the regular quality-trimming algorithm cannot deal with this situation,</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">@@ -79,15 +79,19 @@ Model somehow all the flags that exist for semiglobal alignment. For start of th</td>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">Not degraded and no bases before allowed = anchored.</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext">Degraded and bases before allowed = regular 5'</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">API</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">---</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">* https://github.com/marcelm/cutadapt/labels/API</span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext">Paired-end trimming</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">-------------------</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext">* Could also use a paired-end read merger, then remove adapters with -a and -g</span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">Available<span class="idiff left right">/used</span> letters for command-line options</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">Available letters for command-line options</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext">-----------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">* Remaining characters: All uppercase letters except A, B, G, M, N, O, U</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="plaintext">* Lowercase letters: i, <span class="idiff left right">j, </span>k, s, w</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">* Lowercase letters: i, k, s, w</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">* Planned/reserved: Q (paired-end quality trimming)</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#6677207c6fa30ac9cec19ad036ae842582159ecb"><strong>doc/installation.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -158,5 +158,5 @@ To run Cutadapt and see the version number, type ::</td>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="plaintext"> ~/cutadapt-venv/bin/cutadapt --version</span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext">The reported version number will be something like ``2.2.dev5+gf564208``. This</span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="plaintext">means that you are now running the version of Cutadapt that will become 2.2, and that i<span class="idiff left right">s</span> contains</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">means that you are now running the version of Cutadapt that will become 2.2, and that i<span class="idiff left right">t</span> contains</span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext">5 changes (*commits*) since the previous release (2.1 in this case).</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -102,7 +102,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">''</span><span class="p">:</span> <span class="s" style="color: #d14;">'src'</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(</span><span class="s" style="color: #d14;">'src'</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'cutadapt = cutadapt.__main__:main'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'dnaio<span class="idiff left">>=0.3'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'xopen>=0.7.3</span>'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'dnaio<span class="idiff left">~=0.3.0'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'xopen~=0.8.1</span>'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC106" 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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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'dev'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'Cython'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest'</span><span class="p">,</span> <span class="s" style="color: #d14;">'pytest-timeout'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sphinx_issues'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="p">},</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#babdfe5d368a4907abadce7f9b00dfab2489185a"><strong>src/cutadapt/__main__.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">@@ -64,7 +64,7 @@ from xopen import xopen</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.<span class="idiff left right">adapters</span></span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterParser</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.<span class="idiff left right">parser</span></span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterParser</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">LengthTagModifier</span><span class="p">,</span> <span class="n" style="color: #333;">SuffixRemover</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixSuffixAdder</span><span class="p">,</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">ZeroCapper</span><span class="p">,</span> <span class="n" style="color: #333;">QualityTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">UnconditionalCutter</span><span class="p">,</span> <span class="n" style="color: #333;">NEndTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">PairedAdapterCutterError</span><span class="p">,</span> <span class="n" style="color: #333;">PairedAdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">NextseqQualityTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">Shortener</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">@@ -72,6 +72,7 @@ from cutadapt.report import full_report, minimal_report</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">SingleEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">SerialPipelineRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">available_cpu_count</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup_logging</span><span class="p">,</span> <span class="n" style="color: #333;">REPORT</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC78" 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">@@ -107,50 +108,6 @@ class CommandLineError(Exception):</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Custom log level, see setup_logging</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="n" style="color: #333;">REPORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NiceFormatter</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"><span class="s" style="color: #d14;"> Do not prefix "INFO:" to info-level log messages (but do it for all other</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;"> levels).</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;"> Based on http://stackoverflow.com/a/9218261/715090 .</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">levelno</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span> <span class="n" style="color: #333;">REPORT</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{}: {}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">levelname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC124" 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="o" style="font-weight: 600;">.</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="LC125" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC127" 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;">stdout</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;">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="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC129" 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="LC130" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For --report=minimal, we need this custom log level because we want to</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print nothing except the minimal report and therefore cannot use the</span></span>
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<pre style="margin: 0;">-<span id="LC133" 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="LC134" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Due to backwards compatibility, logging output is sent to standard output</span></span>
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># instead of standard error if the -o option is used.</span></span>
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<pre style="margin: 0;">-<span id="LC138" 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;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stdout</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC139" 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;">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="LC140" 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="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEBUG</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ERROR</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">minimal</span><span class="p">:</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">REPORT</span></span>
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<pre style="margin: 0;">-<span id="LC147" 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="LC148" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span></span>
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<pre style="margin: 0;">-<span id="LC149" 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;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC150" 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;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC151" 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;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">stream_handler</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_argument_parser</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC112" 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;">CutadaptArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">usage</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__doc__</span><span class="p">,</span> <span class="n" style="color: #333;">add_help</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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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">group</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">"Options"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -171,7 +128,7 @@ def get_argument_parser():</td>
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171
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--buffer-size"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4000000</span><span class="p">,</span></span>
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172
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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173
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Compression level for gzipped output files. Not exposed since we have -Z</span></span>
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--compression-level"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--compression-level"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">type</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">6</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Deprecated: The input format is always auto-detected</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-f"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--format"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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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">@@ -588,15 +545,7 @@ def input_files_from_parsed_args(inputs, paired, interleaved):</td>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">input_paired_filename</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>
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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="python"><span class="s" style="color: #d14;"> Setup a processing pipeline from parsed command-line arguments.</span></span>
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<pre style="margin: 0;">-<span id="LC594" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"><span class="s" style="color: #d14;"> If there are any problems parsing the arguments, a CommandLineError is thrown.</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC597" class="line" lang="python"><span class="s" style="color: #d14;"> Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC549" 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;">paired</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_paired_output</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">CommandLineError</span><span class="p">(</span><span class="s" style="color: #d14;">"Option --untrimmed-paired-output can only be used when "</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">@@ -631,6 +580,17 @@ def pipeline_from_parsed_args(args, paired, is_interleaved_output):</td>
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">CommandLineError</span><span class="p">(</span><span class="s" style="color: #d14;">"The overlap must be at least 1."</span><span class="p">)</span></span>
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632
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581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">gc_content</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">100</span><span class="p">):</span></span>
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">CommandLineError</span><span class="p">(</span><span class="s" style="color: #d14;">"GC content must be given as percentage between 0 and 100"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="python"><span class="s" style="color: #d14;"> Setup a processing pipeline from parsed command-line arguments.</span></span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="python"><span class="s" style="color: #d14;"> If there are any problems parsing the arguments, a CommandLineError is raised.</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="python"><span class="s" style="color: #d14;"> Return an instance of Pipeline (SingleEndPipeline or PairedEndPipeline)</span></span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="python"> <span class="n" style="color: #333;">check_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">)</span></span>
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594
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'none'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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596
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<pre style="margin: 0;"> <span id="LC596" 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">@@ -780,7 +740,7 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>
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780
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<pre style="margin: 0;"> <span id="LC740" 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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741
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<pre style="margin: 0;"> <span id="LC741" 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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742
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<pre style="margin: 0;"> <span id="LC742" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handlers</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC783" class="line" lang="python"> <span class="n" style="color: #333;">setup_logging</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>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="python"> <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">logger</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </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>
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784
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744
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<pre style="margin: 0;"> <span id="LC744" 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="o" style="font-weight: 600;">.</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="o" style="font-weight: 600;">.</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">)</span></span>
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745
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">profile</span><span class="p">:</span></span>
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746
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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cProfile</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -820,13 +780,10 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>
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780
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"> <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span></span>
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781
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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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822
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782
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<pre style="margin: 0;"> <span id="LC782" 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="LC823" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">logg</span>er</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Running in parallel is currently not supported for '</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">pars</span>er</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'Running in parallel is currently not supported for '</span></span>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"> <span class="s" style="color: #d14;">'the given combination of command-line parameters.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">These '</span></span>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"> <span class="s" style="color: #d14;">'options are not supported: --info-file, --rest-file, '</span></span>
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<pre style="margin: 0;">-<span id="LC826" class="line" lang="python"> <span class="s" style="color: #d14;">'--wildcard-file, --untrimmed-output, '</span></span>
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<pre style="margin: 0;">-<span id="LC827" class="line" lang="python"> <span class="s" style="color: #d14;">'--untrimmed-paired-output, --too-short-output, '</span></span>
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<pre style="margin: 0;">-<span id="LC828" class="line" lang="python"> <span class="s" style="color: #d14;">'--too-short-paired-output, --too-long-output, '</span></span>
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<pre style="margin: 0;">-<span id="LC829" class="line" lang="python"> <span class="s" style="color: #d14;">'--too-long-paired-output, --format</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="LC786" class="line" lang="python"> <span class="s" style="color: #d14;">'--wildcard-file, --format</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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787
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"> <span class="s" style="color: #d14;">'Also, demultiplexing is not supported.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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831
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"> <span class="s" style="color: #d14;">'Omit --cores/-j to continue.'</span><span class="p">)</span></span>
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789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#3fdf9aa7a8f7f494997913e3e527a05e6d95fa34"><strong>src/cutadapt/_align.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Generated by Cython 0.29.1<span class="idiff left right">2</span> */</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Generated by Cython 0.29.1<span class="idiff left right">3</span> */</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* BEGIN: Cython Metadata</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -20,8 +20,8 @@ END: Cython Metadata */</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#error Cython requires Python 2.6+ or Python 3.3+.</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_ABI "0_29_1<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_HEX_VERSION 0x001D0<span class="idiff left right">C</span>F0</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_ABI "0_29_1<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_HEX_VERSION 0x001D0<span class="idiff left right">D</span>F0</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_FUTURE_DIVISION 1</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef offsetof</span></span>
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<li id="4045e163dd270b4b21bcebce419a3b9ab8ffb64e">
<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#4045e163dd270b4b21bcebce419a3b9ab8ffb64e"><strong>src/cutadapt/_version.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># coding: utf-8</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># file generated by setuptools_scm</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># don't change, don't track in version control</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">4</span>'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">5</span>'</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#8fb347891ec0a40b16ef2bdbe361f823e12aa016"><strong>src/cutadapt/adapters.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">@@ -4,14 +4,11 @@ Adapter finding and trimming classes</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">The ...Adapter classes are responsible for finding adapters.</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="s" style="color: #d14;">The ...Match classes trim the reads.</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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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;">re</span></span>
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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;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">enum</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Enum</span></span>
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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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>
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<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;">dnaio.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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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</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">align</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.align</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">hamming_environment</span></span>
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<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;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">align</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC14" 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">@@ -43,408 +40,6 @@ WHERE_TO_REMOVE_MAP = {</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><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>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterSpecification</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> Description of a single adapter. This represents the same information that would be</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="s" style="color: #d14;"> given on the commandline through an option such as -a, but does not handle linked</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;"> adapters on also not the file: syntax.</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="s" style="color: #d14;"> These are the attributes:</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> - name (None or str)</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> - restriction (None, 'anchored', or 'noninternal')</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> - sequence (nucleotide sequence as string)</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> - parameters (dict with extra parameters such as 'max_error_rate', 'min_overlap')</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> - cmdline_type ('front' for -a, 'back' for -g and 'anywhere' for -b)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> >>> AdapterSpecification.parse('a_name=ACGT;anywhere', 'back')</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;"> AdapterSpecification(name='a_name', restriction=None, sequence='ACGT', parameters={'anywhere': True}, cmdline_type='back')</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC64" 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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">restriction</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parameters</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmdline_type</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</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="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"""Factory for creating an instance from a string specification"""</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cls</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="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="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'{}(name={!r}, restriction={!r}, sequence={!r}, parameters={!r}, cmdline_type={!r})'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> Replace all occurrences of ``x{n}`` (where x is any character) with n</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> occurrences of x. Raise ValueError if the expression cannot be parsed.</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;"> >>> AdapterSpecification.expand_braces('TGA{5}CT')</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"><span class="s" style="color: #d14;"> 'TGAAAAACT'</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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99
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Simple DFA with four states, encoded in prev</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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102
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'([{}])'</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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103
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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105
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" 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;">'"{" must be used after a character'</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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109
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'"}" cannot be used here'</span><span class="p">)</span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" 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;">s</span></span>
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111
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'{'</span><span class="p">:</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">prev</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;">s</span><span class="p">)</span></span>
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114
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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="ow" style="font-weight: 600;">not</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">10000</span><span class="p">:</span></span>
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115
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<pre style="margin: 0;">-<span id="LC115" 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;">'Value {} invalid'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">))</span></span>
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116
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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117
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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118
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<pre style="margin: 0;">-<span id="LC118" 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;">'"}" expected'</span><span class="p">)</span></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">prev</span></span>
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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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122
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC123" 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;">'Expected "{"'</span><span class="p">)</span></span>
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124
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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{'</span></span>
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125
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<pre style="margin: 0;">-<span id="LC125" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if we are in a non-terminating state</span></span>
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126
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<pre style="margin: 0;">-<span id="LC126" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'{'</span><span class="p">:</span></span>
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127
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<pre style="margin: 0;">-<span id="LC127" 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;">"Unterminated expression"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_extract_name</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification given as 'name=adapt' into 'name' and 'adapt'.</span></span>
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134
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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135
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'='</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</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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137
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<pre style="margin: 0;">-<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span></span>
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138
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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140
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<pre style="margin: 0;">-<span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">allowed_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># abbreviations</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">'e'</span><span class="p">:</span> <span class="s" style="color: #d14;">'max_error_rate'</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;">'error_rate'</span><span class="p">:</span> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">'o'</span><span class="p">:</span> <span class="s" style="color: #d14;">'min_overlap'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># allowed parameters</span></span>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</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;">'optional'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># If this is specified, 'required' will be set to False</span></span>
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_parameters</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse key=value;key=value;key=value into a dict"""</span></span>
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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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164
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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">:</span></span>
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165
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">field</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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166
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<pre style="margin: 0;">-<span id="LC166" 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;">field</span><span class="p">:</span></span>
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167
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">equals</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">field</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">'='</span><span class="p">)</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">equals</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;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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170
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<pre style="margin: 0;">-<span id="LC170" 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;">'No value given'</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<td class="diff-line-num old old_line" 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">
172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">'Unknown parameter {}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<pre style="margin: 0;">-<span id="LC174" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># unabbreviate</span></span>
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175
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</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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176
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<pre style="margin: 0;">-<span id="LC176" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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178
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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;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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180
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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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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" 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">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">value</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;">value</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" 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">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">'Key {} specified twice'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">))</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'optional'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'required'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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189
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<pre style="margin: 0;">-<span id="LC189" 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;">"'optional' and 'required' cannot be specified at the same time"</span><span class="p">)</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'optional'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'required'</span><span class="p">]</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="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'optional'</span><span class="p">]</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"></span>
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195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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196
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification for a non-linked adapter (without '...')</span></span>
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199
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"></span>
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200
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> Allow:</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTER</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTERX</span></span>
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTER$</span></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and ADAPTER</span></span>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and XADAPTER</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and ^ADAPTER</span></span>
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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"><span class="s" style="color: #d14;"> 'anywhere' and ADAPTER</span></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"front"</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">,</span> <span class="s" style="color: #d14;">"anywhere"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC210" 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;">"cmdline_type must be front, back or anywhere"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="s" style="color: #d14;">"You cannot use multiple placement restrictions for an adapter at the same time. "</span></span>
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">"Choose one of ^ADAPTER, ADAPTER$, XADAPTER or ADAPTERX"</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;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">parameters_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_extract_name</span><span class="p">(</span><span class="n" style="color: #333;">spec</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;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</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;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_parameters</span><span class="p">(</span><span class="n" style="color: #333;">parameters_spec</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;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Special case for adapters consisting of only X characters:</span></span>
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This needs to be supported for backwards-compatibilitity</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">))</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="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="p">{}</span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'^'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'anchored'</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">front_restriction</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="LC231" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'noninternal'</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'xX'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'$'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'anchored'</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</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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239
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">back_restriction</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="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'noninternal'</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'xX'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">n_placement_restrictions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">front_restriction</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">back_restriction</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n_placement_restrictions</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="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">back_restriction</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC250" 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>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">"Allowed placement restrictions for a 5' adapter are XADAPTER and ^ADAPTER"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">front_restriction</span><span class="p">:</span></span>
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253
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<pre style="margin: 0;">-<span id="LC253" 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>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">"Allowed placement restrictions for a 3' adapter are ADAPTERX and ADAPTER$"</span><span class="p">)</span></span>
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255
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"></span>
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256
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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">front_restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">back_restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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257
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">front_restriction</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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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_restriction</span></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_restriction</span></span>
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261
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">restriction</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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263
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<pre style="margin: 0;">-<span id="LC263" 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>
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264
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"> <span class="s" style="color: #d14;">"Placement restrictions (with X, ^, $) not supported for 'anywhere' (-b) adapters"</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span></span>
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267
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_restriction_to_where</span><span class="p">(</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">):</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span><span class="p">:</span></span>
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271
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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272
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT</span></span>
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273
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">:</span></span>
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274
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">:</span></span>
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276
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT_NOT_INTERNAL</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" 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>
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<td class="diff-line-num old old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
279
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="s" style="color: #d14;">'Value {} for a front restriction not allowed'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">restriction</span><span class="p">))</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;">-<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">:</span></span>
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284
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUFFIX</span></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK_NOT_INTERNAL</span></span>
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<pre style="margin: 0;">-<span id="LC287" 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="LC288" 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>
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289
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="s" style="color: #d14;">'Value {} for a back restriction not allowed'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">restriction</span><span class="p">))</span></span>
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290
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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291
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span></span>
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292
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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293
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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294
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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295
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<pre style="margin: 0;">-<span id="LC295" 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;">'No placement may be specified for "anywhere" adapters'</span><span class="p">)</span></span>
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296
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">where</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="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_restriction_to_where</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterParser</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;"> Factory for Adapter classes that all use the same default parameters (error rate,</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"><span class="s" style="color: #d14;"> indels etc.). The given **kwargs will be passed to the Adapter constructors.</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC306" 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="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="LC307" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># kwargs: max_error_rate, min_overlap, read_wildcards, adapter_wildcards, indels</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification not using ``file:`` notation and return</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> an object of an appropriate Adapter class.</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;"> name -- Adapter name if not included as part of the spec. (If spec is</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;"> 'name=ADAPTER', name will be 'name'.)</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;"> cmdline_type -- describes which commandline parameter was used (``-a``</span></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"><span class="s" style="color: #d14;"> is 'back', ``-b`` is 'anywhere', and ``-g`` is 'front').</span></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'front'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">):</span></span>
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322
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<pre style="margin: 0;">-<span id="LC322" 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;">'cmdline_type cannot be {!r}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">))</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">spec1</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">'...'</span><span class="p">)</span></span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">spec</span></span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"></span>
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326
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<pre style="margin: 0;">-<span id="LC326" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Handle linked adapter</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">middle</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;">spec1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_linked</span><span class="p">(</span><span class="n" style="color: #333;">spec1</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">middle</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'...'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC330" 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;">spec1</span><span class="p">:</span></span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># -a ...ADAPTER</span></span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec2</span></span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># -g ...ADAPTER</span></span>
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334
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<pre style="margin: 0;">-<span id="LC334" 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;">'Invalid adapter specification'</span><span class="p">)</span></span>
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335
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span></span>
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336
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># -a ADAPTER...</span></span>
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337
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'front'</span></span>
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338
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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339
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># -g ADAPTER...</span></span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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<pre style="margin: 0;">-<span id="LC341" 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="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="s" style="color: #d14;">'This should not happen'</span></span>
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<pre style="margin: 0;">-<span id="LC343" 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="LC344" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="python"> <span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC348" 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;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">-<span id="LC351" class="line" lang="python"> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'remove'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WHERE_TO_REMOVE_MAP</span><span class="p">[</span><span class="n" style="color: #333;">where</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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<pre style="margin: 0;">-<span id="LC353" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC354" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC356" 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;">BackOrFrontAdapter</span></span>
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<pre style="margin: 0;">-<span id="LC357" 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="LC358" 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;">Adapter</span></span>
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<pre style="margin: 0;">-<span id="LC359" 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 class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">where</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;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_linked</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return a linked adapter from two specification strings"""</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC365" 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;">"'anywhere' (-b) adapters may not be linked"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">front_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec1</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="LC367" class="line" lang="python"> <span class="n" style="color: #333;">back_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec2</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC368" 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;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">textwrap</span></span>
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<pre style="margin: 0;">-<span id="LC373" 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;">warning</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrap</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="s" style="color: #d14;">"You specified a linked adapter as '-a ADAPTER1...ADAPTER2'. "</span></span>
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<pre style="margin: 0;">-<span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">"The interpretation of what this means has changed in Cutadapt 2.0. "</span></span>
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<pre style="margin: 0;">-<span id="LC376" class="line" lang="python"> <span class="s" style="color: #d14;">"(The 5' adapter is now no longer anchored by default.) "</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="s" style="color: #d14;">"To get results consist with the old behavior, you need to anchor "</span></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"> <span class="s" style="color: #d14;">"the 5' adapter explicitly as in '-a ^ADAPTER1...ADAPTER2'."</span></span>
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<pre style="margin: 0;">-<span id="LC379" class="line" lang="python"> <span class="p">)))</span></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC381" class="line" lang="python"> <span class="n" style="color: #333;">front_anchored</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">back_anchored</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">front_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">front_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">back_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">back_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g requires both adapters to be present</span></span>
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="python"> <span class="n" style="color: #333;">back_required</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="LC393" 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="LC394" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a requires only the anchored adapters to be present</span></span>
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_anchored</span></span>
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_anchored</span></span>
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Handle parameters overriding whether an adapter is required</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'required'</span><span class="p">,</span> <span class="n" style="color: #333;">front_required</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'required'</span><span class="p">,</span> <span class="n" style="color: #333;">back_required</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</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;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">(),</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC403" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</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;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">(),</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC405" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification and yield appropriate Adapter classes.</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"><span class="s" style="color: #d14;"> This works like the _parse_no_file() function above, but also supports the</span></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"><span class="s" style="color: #d14;"> ``file:`` notation for reading adapters from an external FASTA</span></span>
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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python"><span class="s" style="color: #d14;"> file. Since a file can contain multiple adapters, this</span></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"><span class="s" style="color: #d14;"> function is a generator.</span></span>
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<pre style="margin: 0;">-<span id="LC422" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'file:'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read adapter sequences from a file</span></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC426" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC429" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</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;">name</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;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC433" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_multi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="n" style="color: #333;">anywhere</span><span class="p">,</span> <span class="n" style="color: #333;">front</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC434" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"><span class="s" style="color: #d14;"> Parse all three types of commandline options that can be used to</span></span>
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;"> specify adapters. back, anywhere and front are lists of strings,</span></span>
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<pre style="margin: 0;">-<span id="LC437" class="line" lang="python"><span class="s" style="color: #d14;"> corresponding to the respective commandline types (-a, -b, -g).</span></span>
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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;"> Return a list of appropriate Adapter classes.</span></span>
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">specs</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">anywhere</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">front</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="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">specs</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC444" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">adapters</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC447" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">returns_defaultdict_int</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;"># We need this function to make EndStatistics picklable.</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Even a @staticmethod of EndStatistics is not sufficient</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">@@ -1016,7 +611,7 @@ class MultiAdapter:</td>
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters</span><span class="p">:</span></span>
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1017
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"> <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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">k</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;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC1019" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</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 class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hamming_environment</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</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 class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">align</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">hamming_environment</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">k</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">index</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"> <span class="n" style="color: #333;">other_adapter</span><span class="p">,</span> <span class="n" style="color: #333;">other_errors</span><span class="p">,</span> <span class="n" style="color: #333;">other_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]</span></span>
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1022
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">other_matches</span><span class="p">:</span></span>
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<li id="6ed465db6839a69141086c2acf1dc01a8b17a981">
<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#6ed465db6839a69141086c2acf1dc01a8b17a981"><strong>src/cutadapt/filters.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,15 +13,33 @@ filters is created and each redirector is called in turn until one returns True.</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">The read is then assumed to have been "consumed", that is, either written</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">somewhere or filtered (should be discarded).</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABC</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">errno</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">raise_open_files_limit</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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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="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="LC27" 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="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoFilter</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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndFilter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedEndFilter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">+<span id="LC38" 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;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">matches1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">matches2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></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="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoFilter</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="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;"> No filtering, just send each read to the given writer.</span></span>
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<pre style="margin: 0;"> <span id="LC45" 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">@@ -41,7 +59,7 @@ class NoFilter:</td>
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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;">DISCARD</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedNoFilter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedNoFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">PairedEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> No filtering, just send each paired-end read to the given writer.</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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">@@ -62,11 +80,11 @@ class PairedNoFilter:</td>
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<pre style="margin: 0;"> <span id="LC80" 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="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC65" 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>
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<pre style="margin: 0;">+<span id="LC83" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC85" 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>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC69" 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;">writer</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">filter2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC87" 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;">writer</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleEndFilter</span></span><span class="p">,</span> <span class="n" style="color: #333;">filter2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO filter2 should really not be here</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,7 +103,7 @@ class Redirector:</td>
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85
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103
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<pre style="margin: 0;"> <span id="LC103" 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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86
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC88" 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>
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<pre style="margin: 0;">+<span id="LC106" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">PairedEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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89
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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90
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;"> Redirect paired-end reads matching a filtering criterion to a writer.</span></span>
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<pre style="margin: 0;"> <span id="LC109" 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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,7 +159,7 @@ class PairedRedirector:</td>
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141
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TooShortReadFilter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TooShortReadFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC163" 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;">minimum_length</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minimum_length</span></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -149,7 +167,7 @@ class TooShortReadFilter:</td>
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149
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167
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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="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minimum_length</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"></span>
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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="LC152" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TooLongReadFilter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TooLongReadFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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153
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171
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<pre style="margin: 0;"> <span id="LC171" 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;">maximum_length</span><span class="p">):</span></span>
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154
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maximum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maximum_length</span></span>
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155
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,7 +175,7 @@ class TooLongReadFilter:</td>
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157
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maximum_length</span></span>
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158
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"></span>
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159
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"></span>
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160
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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NContentFilter</span><span class="p">:</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NContentFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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161
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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162
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"><span class="s" style="color: #d14;"> Discards a reads that has a number of 'N's over a given threshold. It handles both raw counts</span></span>
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163
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"><span class="s" style="color: #d14;"> of Ns as well as proportions. Note, for raw counts, it is a 'greater than' comparison,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</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">@@ -183,7 +201,7 @@ class NContentFilter:</td>
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183
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n_count</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff</span></span>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"></span>
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscardUntrimmedFilter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscardUntrimmedFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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187
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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188
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;"> Return True if read is untrimmed.</span></span>
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189
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<pre style="margin: 0;"> <span id="LC207" 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="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="209" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -191,7 +209,7 @@ class DiscardUntrimmedFilter:</td>
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191
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">matches</span></span>
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192
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscardTrimmedFilter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscardTrimmedFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"> Return True if read is trimmed.</span></span>
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -199,7 +217,7 @@ class DiscardTrimmedFilter:</td>
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199
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">bool</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="LC218" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CasavaFilter</span><span class="p">:</span></span>
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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;">CasavaFilter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"><span class="s" style="color: #d14;"> Remove reads that fail the CASAVA filter. These have header lines that</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"><span class="s" style="color: #d14;"> look like ``xxxx x:Y:x:x`` (with a ``Y``). Reads that pass the filter</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">@@ -212,7 +230,23 @@ class CasavaFilter:</td>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">right</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">':Y:'</span> <span class="c1" style="color: #998; font-style: italic;"># discard if :Y: found</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Demultiplexer</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;"> Open a FASTA/FASTQ file for writing. If it fails because the number of open files</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;"> would be exceeded, try to raise the soft limit and re-try.</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OSError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex trimmed reads. Reads are written to different output files</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;"> depending on which adapter matches. Files are created when the first read</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,15 +275,15 @@ class Demultiplexer:</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">dnaio</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">replace</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'{name}'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff right">),</span></span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">mode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'w'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_open_raise_limit</span></span><span class="p"><span class="idiff right">(</span></span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">template</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">replace</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'{name}'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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247
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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248
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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249
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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250
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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251
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">dnaio</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">untrimmed_path</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">mode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'w'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">qualities</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">=</span></span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">_open_raise_limit</span></span><span class="p"><span class="idiff right">(</span></span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">untrimmed_path</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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253
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,7 +297,7 @@ class Demultiplexer:</td>
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedDemultiplexer</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedDemultiplexer</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">PairedEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex trimmed paired-end reads. Reads are written to different output files</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;"> depending on which adapter (in read 1) matches.</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">@@ -298,7 +332,7 @@ class PairedDemultiplexer:</td>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CombinatorialDemultiplexer</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CombinatorialDemultiplexer</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">PairedEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex reads depending on which adapter matches, taking into account both matches</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"><span class="s" style="color: #d14;"> on R1 and R2.</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">@@ -331,7 +365,6 @@ class CombinatorialDemultiplexer:</td>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;"> Write the read to the proper output file according to the most recent matches both on</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;"> R1 and R2</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># import ipdb; ipdb.set_trace()</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">read2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches1</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches1</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches2</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches2</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</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">@@ -346,8 +379,8 @@ class CombinatorialDemultiplexer:</td>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"> <span class="n" style="color: #333;">path2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_path</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">dnaio</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'w'</span></span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">dnaio</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">open</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">path2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mode</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'w'</span></span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">_open_raise_limit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">path1</span></span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">_open_raise_limit</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">path2</span></span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="p">)</span></span>
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352
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">writer1</span><span class="p">,</span> <span class="n" style="color: #333;">writer2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -363,7 +396,7 @@ class CombinatorialDemultiplexer:</td>
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363
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"> <span class="n" style="color: #333;">w2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"></span>
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398
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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="LC366" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RestFileWriter</span><span class="p">:</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RestFileWriter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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400
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<pre style="margin: 0;"> <span id="LC400" 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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368
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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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369
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402
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -375,7 +408,7 @@ class RestFileWriter:</td>
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375
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408
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<pre style="margin: 0;"> <span id="LC408" 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="LC409" class="line" lang="python"></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WildcardFileWriter</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WildcardFileWriter</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC412" 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="LC413" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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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414
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<pre style="margin: 0;"> <span id="LC414" 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">@@ -385,7 +418,7 @@ class WildcardFileWriter:</td>
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<pre style="margin: 0;"> <span id="LC418" 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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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"></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="LC388" 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>
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<pre style="margin: 0;">+<span id="LC421" 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 class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">SingleEndFilter</span></span><span class="p"><span class="idiff right">)</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC422" 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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390
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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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391
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae"><strong>src/cutadapt/log.py</strong></a>
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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>
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2
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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;">logging</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Custom log level</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">REPORT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">25</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NiceFormatter</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="s" style="color: #d14;"> Do not prefix "INFO:" to info-level log messages (but do it for all other</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="s" style="color: #d14;"> levels).</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;"> Based on http://stackoverflow.com/a/9218261/715090 .</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="LC17" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">levelno</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span><span class="p">,</span> <span class="n" style="color: #333;">REPORT</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{}: {}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">levelname</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" 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="o" style="font-weight: 600;">.</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="LC20" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" 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;">stdout</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;">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="bp" style="color: #999;">False</span><span class="p">):</span></span>
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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;"> Attach handler to the global logger object</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># For --report=minimal, we need this custom log level because we want to</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># print nothing except the minimal report and therefore cannot use the</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;"># INFO level (and the ERROR level would give us an 'ERROR:' prefix).</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Due to backwards compatibility, logging output is sent to standard output</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># instead of standard error if the -o option is used.</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stdout</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" 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;">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="LC35" 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="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEBUG</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ERROR</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">minimal</span><span class="p">:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">REPORT</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">INFO</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" 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;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="p">)</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" 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;">setLevel</span><span class="p">(</span><span class="n" style="color: #333;">level</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">addHandler</span><span class="p">(</span><span class="n" style="color: #333;">stream_handler</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5"><strong>src/cutadapt/parser.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Parse adapter specifications</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio.readers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FastaReader</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">WHERE_TO_REMOVE_MAP</span><span class="p">,</span> <span class="n" style="color: #333;">Adapter</span><span class="p">,</span> <span class="n" style="color: #333;">BackOrFrontAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterSpecification</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;"> Description of a single non-linked adapter.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;"> These are the attributes:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> - name (None or str)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> - restriction (None, 'anchored', or 'noninternal')</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> - sequence (nucleotide sequence as string)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="s" style="color: #d14;"> - parameters (dict with extra parameters such as 'max_error_rate', 'min_overlap')</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> - cmdline_type ('front' for -a, 'back' for -g and 'anywhere' for -b)</span></span>
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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="s" style="color: #d14;"> >>> AdapterSpecification.parse('a_name=ACGT;anywhere', 'back')</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> AdapterSpecification(name='a_name', restriction=None, sequence='ACGT', parameters={'anywhere': True}, cmdline_type='back')</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> """</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="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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"anchored"</span><span class="p">,</span> <span class="s" style="color: #d14;">"noninternal"</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;">assert</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">in</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 class="s" style="color: #d14;">"anywhere"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">restriction</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parameters</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cmdline_type</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</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="LC39" class="line" lang="python"> <span class="s" style="color: #d14;">"""Factory for creating an instance from a string specification"""</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cls</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__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="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'{}(name={!r}, restriction={!r}, sequence={!r}, parameters={!r}, cmdline_type={!r})'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__class__</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__name__</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span></span>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" 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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57
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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;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> Replace all occurrences of ``x{n}`` (where x is any character) with n</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> occurrences of x. Raise ValueError if the expression cannot be parsed.</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="s" style="color: #d14;"> >>> AdapterSpecification.expand_braces('TGA{5}CT')</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="s" style="color: #d14;"> 'TGAAAAACT'</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Simple DFA with four states, encoded in prev</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">''</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'([{}])'</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" 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;">'"{" must be used after a character'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">'"}" cannot be used here'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" 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;">s</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">s</span></span>
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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'{'</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">prev</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;">s</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">10000</span><span class="p">:</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" 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;">'Value {} invalid'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">))</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" 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;">'"}" expected'</span><span class="p">)</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">result</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">prev</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="p">:</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" 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;">'Expected "{"'</span><span class="p">)</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{'</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check if we are in a non-terminating state</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'{'</span><span class="p">:</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" 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;">"Unterminated expression"</span><span class="p">)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"></span>
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96
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<pre style="margin: 0;">+<span id="LC96" 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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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_extract_name</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification given as 'name=adapt' into 'name' and 'adapt'.</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'='</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">fields</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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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fields</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">allowed_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># abbreviations</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="s" style="color: #d14;">'e'</span><span class="p">:</span> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">,</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="s" style="color: #d14;">'error_rate'</span><span class="p">:</span> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">,</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="s" style="color: #d14;">'o'</span><span class="p">:</span> <span class="s" style="color: #d14;">'min_overlap'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># allowed parameters</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">'optional'</span><span class="p">:</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># If this is specified, 'required' will be set to False</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_parameters</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="s" style="color: #d14;">"""Parse key=value;key=value;key=value into a dict"""</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fields</span><span class="p">:</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">field</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" 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;">field</span><span class="p">:</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">equals</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">field</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">'='</span><span class="p">)</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">equals</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;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" 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;">'No value given'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">'Unknown parameter {}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="c1" style="color: #998; font-style: italic;"># unabbreviate</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</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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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">allowed_parameters</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">value</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;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">(</span><span class="s" style="color: #d14;">'Key {} specified twice'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'optional'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'required'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" 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;">"'optional' and 'required' cannot be specified at the same time"</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'optional'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">result</span><span class="p">:</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'required'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">result</span><span class="p">[</span><span class="s" style="color: #d14;">'optional'</span><span class="p">]</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification for a non-linked adapter (without '...')</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"><span class="s" style="color: #d14;"> Allow:</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTER</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTERX</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;"> 'back' and ADAPTER$</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and ADAPTER</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and XADAPTER</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"><span class="s" style="color: #d14;"> 'front' and ^ADAPTER</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"><span class="s" style="color: #d14;"> 'anywhere' and ADAPTER</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"front"</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">,</span> <span class="s" style="color: #d14;">"anywhere"</span><span class="p">):</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" 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;">"cmdline_type must be front, back or anywhere"</span><span class="p">)</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">error</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"You cannot use multiple placement restrictions for an adapter at the same time. "</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"Choose one of ^ADAPTER, ADAPTER$, XADAPTER or ADAPTERX"</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">parameters_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">';'</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_extract_name</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cls</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_parameters</span><span class="p">(</span><span class="n" style="color: #333;">parameters_spec</span><span class="p">)</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">)</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="python"></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Special case for adapters consisting of only X characters:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This needs to be supported for backwards-compatibilitity</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">))</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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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="p">{}</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'^'</span><span class="p">):</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'anchored'</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:]</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">):</span></span>
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196
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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;">front_restriction</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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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">front_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'noninternal'</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'xX'</span><span class="p">)</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="python"></span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'$'</span><span class="p">):</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'anchored'</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</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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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">'X'</span><span class="p">):</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">back_restriction</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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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">back_restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'noninternal'</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstrip</span><span class="p">(</span><span class="s" style="color: #d14;">'xX'</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">n_placement_restrictions</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">front_restriction</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">back_restriction</span><span class="p">))</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n_placement_restrictions</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">error</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">back_restriction</span><span class="p">:</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" 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>
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<td class="diff-line-num new new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">"Allowed placement restrictions for a 5' adapter are XADAPTER and ^ADAPTER"</span><span class="p">)</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">front_restriction</span><span class="p">:</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" 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>
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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="s" style="color: #d14;">"Allowed placement restrictions for a 3' adapter are ADAPTERX and ADAPTER$"</span><span class="p">)</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">front_restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">back_restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">front_restriction</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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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_restriction</span></span>
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<pre style="margin: 0;">+<span id="LC225" 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="LC226" class="line" lang="python"> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_restriction</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">restriction</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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229
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<pre style="margin: 0;">+<span id="LC229" 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>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">"Placement restrictions (with X, ^, $) not supported for 'anywhere' (-b) adapters"</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">parameters</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>
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234
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<pre style="margin: 0;">+<span id="LC234" 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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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_restriction_to_where</span><span class="p">(</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="n" style="color: #333;">restriction</span><span class="p">):</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span><span class="p">:</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">:</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">:</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT_NOT_INTERNAL</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" 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>
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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="s" style="color: #d14;">'Value {} for a front restriction not allowed'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">restriction</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUFFIX</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">restriction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">:</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK_NOT_INTERNAL</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="s" style="color: #d14;">'Value {} for a back restriction not allowed'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">restriction</span><span class="p">))</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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261
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<pre style="margin: 0;">+<span id="LC261" 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;">'No placement may be specified for "anywhere" adapters'</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">where</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_restriction_to_where</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span><span class="p">)</span></span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python"></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterParser</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"><span class="s" style="color: #d14;"> Factory for Adapter classes that all use the same default parameters (error rate,</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"><span class="s" style="color: #d14;"> indels etc.). The given **kwargs will be passed to the Adapter constructors.</span></span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC272" 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="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="LC273" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># kwargs: max_error_rate, min_overlap, read_wildcards, adapter_wildcards, indels</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification not using ``file:`` notation and return</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="s" style="color: #d14;"> an object of an appropriate Adapter class.</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> name -- Adapter name if not included as part of the spec. (If spec is</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> 'name=ADAPTER', name will be 'name'.)</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="s" style="color: #d14;"> cmdline_type -- describes which commandline parameter was used (``-a``</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;"> is 'back', ``-b`` is 'anywhere', and ``-g`` is 'front').</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'front'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC288" 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;">'cmdline_type cannot be {!r}'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cmdline_type</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">spec1</span><span class="p">,</span> <span class="n" style="color: #333;">middle</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">'...'</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">middle</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;">spec1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_linked</span><span class="p">(</span><span class="n" style="color: #333;">spec1</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">middle</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'...'</span><span class="p">:</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_normalize_ellipsis</span><span class="p">(</span><span class="n" style="color: #333;">spec1</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_not_linked</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>
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299
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<pre style="margin: 0;">+<span id="LC299" 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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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_normalize_ellipsis</span><span class="p">(</span><span class="n" style="color: #333;">spec1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spec1</span><span class="p">:</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a ...ADAPTER</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec2</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g ...ADAPTER</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" 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;">'Invalid adapter specification'</span><span class="p">)</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span></span>
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309
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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;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span><span class="p">:</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a ADAPTER...</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="python"> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'front'</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g ADAPTER...</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec1</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" 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="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Expected either spec1 or spec2"</span><span class="p">)</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_not_linked</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">()</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" 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;">name</span><span class="p">:</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</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>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">[</span><span class="s" style="color: #d14;">'remove'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WHERE_TO_REMOVE_MAP</span><span class="p">[</span><span class="n" style="color: #333;">where</span><span class="p">]</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">where</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">FRONT</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC331" 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;">BackOrFrontAdapter</span></span>
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<pre style="margin: 0;">+<span id="LC332" 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="LC333" 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;">Adapter</span></span>
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<pre style="margin: 0;">+<span id="LC334" 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 class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">where</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;">name</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_parse_linked</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec1</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">spec2</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return a linked adapter from two specification strings"""</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC340" 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;">"'anywhere' (-b) adapters may not be linked"</span><span class="p">)</span></span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">front_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec1</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="LC342" class="line" lang="python"> <span class="n" style="color: #333;">back_spec</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec2</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">name</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'back'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">textwrap</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" 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;">warning</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;">join</span><span class="p">(</span><span class="n" style="color: #333;">textwrap</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrap</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">"You specified a linked adapter as '-a ADAPTER1...ADAPTER2'. "</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="python"> <span class="s" style="color: #d14;">"The interpretation of what this means has changed in Cutadapt 2.0. "</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="python"> <span class="s" style="color: #d14;">"(The 5' adapter is now no longer anchored by default.) "</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="s" style="color: #d14;">"To get results consist with the old behavior, you need to anchor "</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"> <span class="s" style="color: #d14;">"the 5' adapter explicitly as in '-a ^ADAPTER1...ADAPTER2'."</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">front_anchored</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">back_anchored</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">restriction</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">front_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">front_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">back_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">default_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">back_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parameters</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'front'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g requires both adapters to be present</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">front_required</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="LC367" class="line" lang="python"> <span class="n" style="color: #333;">back_required</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="LC368" 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="LC369" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a requires only the anchored adapters to be present</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_anchored</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_anchored</span></span>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Handle parameters overriding whether an adapter is required</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'required'</span><span class="p">,</span> <span class="n" style="color: #333;">front_required</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">back_parameters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="s" style="color: #d14;">'required'</span><span class="p">,</span> <span class="n" style="color: #333;">back_required</span><span class="p">)</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</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;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">(),</span> <span class="n" style="color: #333;">name</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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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">front_parameters</span><span class="p">)</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</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;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span><span class="p">(),</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">back_parameters</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="python"></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">(</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">front_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">back_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="p">)</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">):</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"><span class="s" style="color: #d14;"> Parse an adapter specification and yield appropriate Adapter classes.</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"><span class="s" style="color: #d14;"> This works like the _parse_no_file() function above, but also supports the</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="python"><span class="s" style="color: #d14;"> ``file:`` notation for reading adapters from an external FASTA</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="python"><span class="s" style="color: #d14;"> file. Since a file can contain multiple adapters, this</span></span>
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"><span class="s" style="color: #d14;"> function is a generator.</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 class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">spec</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'file:'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read adapter sequences from a file</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">FastaReader</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">:])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">name</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</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;">name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC405" 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="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">parse_multi</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="n" style="color: #333;">anywhere</span><span class="p">,</span> <span class="n" style="color: #333;">front</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"><span class="s" style="color: #d14;"> Parse all three types of commandline options that can be used to</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="python"><span class="s" style="color: #d14;"> specify adapters. back, anywhere and front are lists of strings,</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="python"><span class="s" style="color: #d14;"> corresponding to the respective commandline types (-a, -b, -g).</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="python"><span class="s" style="color: #d14;"> Return a list of appropriate Adapter classes.</span></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">specs</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">anywhere</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">),</span> <span class="p">(</span><span class="n" style="color: #333;">front</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="LC418" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">specs</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;">adapters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">extend</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">adapters</span></span></pre>
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<li id="1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">
<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#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">@@ -13,7 +13,7 @@ from xopen import xopen</td>
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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;">dnaio</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="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>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PairedModifier</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Modifier</span></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">PairedModifier</span></span>
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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;">.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Statistics</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.filters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Redirector</span><span class="p">,</span> <span class="n" style="color: #333;">PairedRedirector</span><span class="p">,</span> <span class="n" style="color: #333;">NoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedNoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFileWriter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">RestFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">TooShortReadFilter</span><span class="p">,</span> <span class="n" style="color: #333;">TooLongReadFilter</span><span class="p">,</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,26 +35,28 @@ class OutputFiles:</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> The attributes are open file-like objects except when demultiplex is True. In that case,</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> untrimmed, untrimmed2, out and out2 are file names or templates</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> as required by the used demultiplexer ('{name}' etc.).</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> If interleaved is True, then out is written interleaved.</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;"> Files may also be None.</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO interleaving for the other file pairs (too_short, too_long, untrimmed)?</span></span>
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<pre style="margin: 0;"> <span id="LC44" 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="LC43" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">out2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">untrimmed</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">untrimmed2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">too_short</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">too_short2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">too_long</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">too_long2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">rest</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">wildcard</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">demultiplex</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="LC56" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">interleaved</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="LC57" class="line" lang="python"> <span class="idiff left right"> </span><span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</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;">out</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">out2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">untrimmed</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">untrimmed2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">too_short</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">too_short2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">too_long</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">too_long2</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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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">info</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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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">rest</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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">wildcard</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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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">demultiplex</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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">interleaved</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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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">force_fasta</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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58
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="p">):</span></span>
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -94,7 +96,7 @@ class Pipeline(ABC):</td>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_close_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left right">[]</span></span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span></span>
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98
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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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99
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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100
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,11 +109,12 @@ class Pipeline(ABC):</td>
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107
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_untrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">set_input</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infiles</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">In</span>putFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left">connect_io</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">infiles</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">InputFiles</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">outfiles</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Out</span>putFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">infiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interleaved</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_set_output</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_open_writer</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 class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_open_writer</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 class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">,</span> <span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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="LC118" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO backwards-incompatible change (?) would be to use outfiles.interleaved</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># for all outputs</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">force_fasta</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -119,33 +122,33 @@ class Pipeline(ABC):</td>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">file</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">uses_qualities</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"></span>
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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;">set_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;"><span class="idiff left right">_</span>set_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfiles</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">filter_wrapper</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filter_wrapper</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC127" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">RestFileWriter</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;">rest</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">InfoFileWriter</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;">info</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filter_class</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">RestFileWriter</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;">rest</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">InfoFileWriter</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;">info</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfile</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">),</span> <span class="bp" style="color: #999;">None</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># minimum length and maximum length</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">lengths</span><span class="p">,</span> <span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">,</span> <span class="n" style="color: #333;">filter_class</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minimum_length</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;">too_short</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;">too_short2</span><span class="p">,</span> <span class="n" style="color: #333;">TooShortReadFilter</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maximum_length</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;">too_long</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;">too_long2</span><span class="p">,</span> <span class="n" style="color: #333;">TooLongReadFilter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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140
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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="n" style="color: #333;">lengths</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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141
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file1</span><span class="p">:</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_open_writer</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">)</span></span>
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143
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</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="LC145" class="line" lang="python"> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC146" 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="LC147" class="line" lang="python"> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">filter2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f2</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lengths</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_open_writer</span><span class="p">(</span><span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file1</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</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="LC148" class="line" lang="python"> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter_class</span><span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">filter2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">f2</span><span class="p">))</span></span>
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149
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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150
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</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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151
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -251,7 +254,8 @@ class SingleEndPipeline(Pipeline):</td>
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251
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Redirector</span></span>
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252
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>
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253
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_final_filter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_open_writer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span><span class="p">,</span> <span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">force_fasta</span><span class="p">)</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_open_writer</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">force_fasta</span><span class="p">)</span></span>
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255
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">NoFilter</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">)</span></span>
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256
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"></span>
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257
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_create_demultiplexer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); 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="287" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -283,13 +287,10 @@ class PairedEndPipeline(Pipeline):</td>
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283
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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284
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>
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285
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">pair_filter_mode</span><span class="p">):</span></span>
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286
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;"> Setting modify_first_read_only to True enables "legacy mode"</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pair_filter_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair_filter_mode</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Whether to gnore pair_filter mode for discard-untrimmed filter</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Whether to <span class="idiff left right">i</span>gnore pair_filter mode for discard-untrimmed filter</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">override_untrimmed_pair_filter</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="LC295" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier1</span><span class="p">,</span> <span class="n" style="color: #333;">modifier2</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">@@ -396,6 +397,15 @@ def reader_process(file, file2, connections, queue, buffer_size, stdin_fd):</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"><span class="s" style="color: #d14;"> and finally sends "poison pills" (the value -1) to all connections.</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"></span>
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401
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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;">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="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="n" style="color: #333;">worker_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queue</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">connection</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connections</span><span class="p">[</span><span class="n" style="color: #333;">worker_index</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python"> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">chunk1</span><span class="p">)</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chunk2</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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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">connection</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">chunk2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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>
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fdopen</span><span class="p">(</span><span class="n" style="color: #333;">stdin_fd</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">@@ -404,19 +414,10 @@ def reader_process(file, file2, connections, queue, buffer_size, stdin_fd):</td>
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file2</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">xopen</span><span class="p">(</span><span class="n" style="color: #333;">file2</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>
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406
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<pre style="margin: 0;"> <span id="LC416" 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 class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</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="n" style="color: #333;">buffer_size</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Determine the worker that should get this chunk</span></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">worker_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queue</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connections</span><span class="p">[</span><span class="n" style="color: #333;">worker_index</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC411" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">chunk1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">chunk2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="python"> <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>
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<pre style="margin: 0;"> <span id="LC418" 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="LC419" 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="n" style="color: #333;">chunk</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_chunks</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">)):</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Determine the worker that should get this chunk</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="python"> <span class="n" style="color: #333;">worker_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">queue</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connections</span><span class="p">[</span><span class="n" style="color: #333;">worker_index</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC418" class="line" lang="python"> <span class="n" style="color: #333;">pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</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;">pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">chunk</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="python"> <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;">chunk</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Send poison pills to all workers</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">connections</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">@@ -437,13 +438,12 @@ class WorkerProcess(Process):</td>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"><span class="s" style="color: #d14;"> To notify the reader process that it wants data, it puts its own identifier into the</span></span>
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;"> need_work_queue before attempting to read data from the read_pipe.</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC440" 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;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">input_path1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">input_path2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC441" 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;">id_</span><span class="p">,</span> <span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">two_input_files</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">interleaved_input</span><span class="p">,</span> <span class="n" style="color: #333;">orig_outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">read_pipe</span><span class="p">,</span> <span class="n" style="color: #333;">write_pipe</span><span class="p">,</span> <span class="n" style="color: #333;">need_work_queue</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">id_</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline</span></span>
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<pre style="margin: 0;">-<span id="LC445" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_path1</span></span>
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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">input_path2</span></span>
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_two_input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">two_input_files</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved_input</span></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_outfiles</span></span>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_pipe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read_pipe</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">@@ -466,45 +466,13 @@ class WorkerProcess(Process):</td>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">e</span></span>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Setting the .buffer.name attributess below is necessary because</span></span>
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<pre style="margin: 0;">-<span id="LC470" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file format detection uses the file name</span></span>
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<pre style="margin: 0;">-<span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv_bytes</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC472" 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;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC473" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path1</span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path2</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv_bytes</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">input2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">input2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path2</span></span>
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<pre style="margin: 0;">-<span id="LC479" 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="LC480" class="line" lang="python"> <span class="n" style="color: #333;">input2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC481" 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;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC482" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</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="LC485" class="line" lang="python"> <span class="n" style="color: #333;">output2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="python"> <span class="n" style="color: #333;">output2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">-<span id="LC487" 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="LC488" class="line" lang="python"> <span class="n" style="color: #333;">output2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC490" 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;">InputFiles</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">input2</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">(</span><span class="n" style="color: #333;">out</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;">out2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">output2</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">interleaved</span><span class="p">,</span> <span class="n" style="color: #333;">force_fasta</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">force_fasta</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_input</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_output</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"> <span class="n" style="color: #333;">infiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_input_files</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="python"> <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_output_files</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">connect_io</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bp1</span><span class="p">,</span> <span class="n" style="color: #333;">bp2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">process_reads</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="python"> <span class="n" style="color: #333;">cur_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Statistics</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collect</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">bp1</span><span class="p">,</span> <span class="n" style="color: #333;">bp2</span><span class="p">,</span> <span class="p">[],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="python"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cur_stats</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC498" 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;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"> <span class="n" style="color: #333;">processed_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># no. of reads processed in this chunk</span></span>
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">processed_chunk</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">out2</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="LC505" class="line" lang="python"> <span class="n" style="color: #333;">output2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">processed_chunk2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">processed_chunk2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_send_outfiles</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">chunk_index</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span></span>
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"> <span class="n" style="color: #333;">modifier_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Statistics</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">collect</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">,</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">@@ -515,6 +483,47 @@ class WorkerProcess(Process):</td>
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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</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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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">((</span><span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">format_exc</span><span class="p">()))</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_make_input_files</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="LC487" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv_bytes</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC488" 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;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_two_input_files</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">data</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">recv_bytes</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="python"> <span class="n" style="color: #333;">input2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC493" 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="LC494" class="line" lang="python"> <span class="n" style="color: #333;">input2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">(</span><span class="nb" style="color: #0086b3;">input</span><span class="p">,</span> <span class="n" style="color: #333;">input2</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_make_output_files</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="LC498" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="python"><span class="s" style="color: #d14;"> Using self._orig_outfiles as a template, make a new OutputFiles instance</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"><span class="s" style="color: #d14;"> that has BytesIO instances for each non-None output file</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="python"> <span class="n" style="color: #333;">output_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">copy</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO info, rest, wildcard need to be StringIO()</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">attr</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="python"> <span class="s" style="color: #d14;">"out"</span><span class="p">,</span> <span class="s" style="color: #d14;">"out2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"untrimmed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"untrimmed2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_short"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_short2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"too_long"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="python"> <span class="s" style="color: #d14;">"too_long2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"info"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rest"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wildcard"</span></span>
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="python"> <span class="p">):</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">orig_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">)</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">orig_outfile</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="LC510" 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;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" 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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_outfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">output_files</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_files</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_send_outfiles</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">chunk_index</span><span class="p">,</span> <span class="n" style="color: #333;">n_reads</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">chunk_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send</span><span class="p">(</span><span class="n" style="color: #333;">n_reads</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="n" style="color: #333;">processed_chunk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getvalue</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_write_pipe</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">send_bytes</span><span class="p">(</span><span class="n" style="color: #333;">processed_chunk</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">OrderedChunkWriter</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC529" 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">@@ -527,10 +536,10 @@ class OrderedChunkWriter:</td>
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_current_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">chunk_</span>index</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">index</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC533" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_chunks</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">chunk_</span>index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span></span>
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542
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_chunks</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span></span>
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534
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_current_index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_chunks</span><span class="p">:</span></span>
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535
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_chunks</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_current_index</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"> <span class="k" style="font-weight: 600;">del</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_chunks</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_current_index</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">@@ -561,7 +570,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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571
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"><span class="s" style="color: #d14;"> Run a Pipeline in parallel</span></span>
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC564" class="line" lang="python"><span class="s" style="color: #d14;"> - When <span class="idiff left right">set_input</span>() is called, a reader process is spawned.</span></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"><span class="s" style="color: #d14;"> - When <span class="idiff left right">connect_io</span>() is called, a reader process is spawned.</span></span>
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<pre style="margin: 0;"> <span id="LC574" class="line" lang="python"><span class="s" style="color: #d14;"> - When run() is called, as many worker processes as requested are spawned.</span></span>
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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python"><span class="s" style="color: #d14;"> - In the main process, results are written to the output files in the correct</span></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"><span class="s" style="color: #d14;"> order, and statistics are aggregated.</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">@@ -592,8 +601,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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601
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># the workers read from these</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader_process</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC595" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC596" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_two_input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_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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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="603" style="width: 35px; color: rgba(0,0,0,0.3); 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="611" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -603,9 +611,8 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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603
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"></span>
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604
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612
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<pre style="margin: 0;"> <span id="LC612" 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 class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">file1</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">interleaved</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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605
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613
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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader_process</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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606
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<pre style="margin: 0;">-<span id="LC606" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">'Do not call set_input more than once'</span><span class="p">)</span></span>
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607
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<pre style="margin: 0;">-<span id="LC607" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file1</span> <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;">file1</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">str</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">file1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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608
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<pre style="margin: 0;">-<span id="LC608" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_input_path2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file2</span> <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;">file2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="nb" style="color: #0086b3;">str</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">file2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">RuntimeError</span><span class="p">(</span><span class="s" style="color: #d14;">'Do not call connect_io more than once'</span><span class="p">)</span></span>
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615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_two_input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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609
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved</span></span>
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610
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"> <span class="n" style="color: #333;">connections</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Pipe</span><span class="p">(</span><span class="n" style="color: #333;">duplex</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_n_workers</span><span class="p">)]</span></span>
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611
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipes</span><span class="p">,</span> <span class="n" style="color: #333;">connw</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">connections</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="627" style="width: 35px; color: rgba(0,0,0,0.3); 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="634" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -627,12 +634,6 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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627
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634
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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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628
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635
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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629
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636
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcard</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC630" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_short</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC631" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_short2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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632
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<pre style="margin: 0;">-<span id="LC632" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_long</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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633
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<pre style="margin: 0;">-<span id="LC633" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_long2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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634
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC635" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="python"> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">outfiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">demultiplex</span></span>
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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python"></span>
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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>
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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">@@ -649,7 +650,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"> <span class="n" style="color: #333;">connections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">conn_r</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"> <span class="n" style="color: #333;">worker</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">WorkerProcess</span><span class="p">(</span></span>
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652
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC652" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_<span class="idiff left">input_path1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_input_path2</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC653" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_<span class="idiff left right">two_input_files</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_interleaved_input</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipes</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">],</span> <span class="n" style="color: #333;">conn_w</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_need_work_queue</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python"> <span class="n" style="color: #333;">worker</span><span class="o" style="font-weight: 600;">.</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>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -660,7 +661,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC661" 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="LC662" class="line" lang="python"> <span class="n" style="color: #333;">workers</span><span class="p">,</span> <span class="n" style="color: #333;">connections</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_start_workers</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="python"> <span class="n" style="color: #333;">writers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">outfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p"><span class="idiff left">[</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_outfiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">out</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_outfiles</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">out2</span></span><span class="p"><span class="idiff right">]</span>:</span></span>
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">outfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">_outfiles</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python"> <span class="n" style="color: #333;">writers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">OrderedChunkWriter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</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">@@ -730,8 +731,7 @@ class SerialPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC732" 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;">pipeline</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;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC733" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_input</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC734" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_output</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">connect_io</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC736" 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="LC737" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">total1_bp</span><span class="p">,</span> <span class="n" style="color: #333;">total2_bp</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">process_reads</span><span class="p">(</span><span class="n" style="color: #333;">progress</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_progress</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#9ba37233f76e56f10585b4e480e28b5cc079a733"><strong>src/cutadapt/qualtrim.c</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Generated by Cython 0.29.1<span class="idiff left right">2</span> */</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Generated by Cython 0.29.1<span class="idiff left right">3</span> */</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">{</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">@@ -19,8 +19,8 @@ END: Cython Metadata */</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03030000)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"> <span class="cp" style="color: #999; font-weight: 600;">#error Cython requires Python 2.6+ or Python 3.3+.</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_ABI "0_29_1<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_HEX_VERSION 0x001D0<span class="idiff left right">C</span>F0</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_ABI "0_29_1<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_HEX_VERSION 0x001D0<span class="idiff left right">D</span>F0</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define CYTHON_FUTURE_DIVISION 1</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include <stddef.h></span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef offsetof</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#af95dfcb30a51908f338d0fd6a196b9e4c108046"><strong>src/cutadapt/utils.py</strong></a>
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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;">re</span></span>
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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>
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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;">time</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">resource</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;">multiprocessing</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" 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">@@ -27,6 +28,12 @@ def available_cpu_count():</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">multiprocessing</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cpu_count</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" 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;">raise_open_files_limit</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">soft</span><span class="p">,</span> <span class="n" style="color: #333;">hard</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getrlimit</span><span class="p">(</span><span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">RLIMIT_NOFILE</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="n" style="color: #333;">soft</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">setrlimit</span><span class="p">(</span><span class="n" style="color: #333;">resource</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">RLIMIT_NOFILE</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">soft</span><span class="p">,</span> <span class="n" style="color: #333;">hard</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Progress</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;"> Write progress</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#4c91f80a781e5621e92c74fdd1bddaa8ef6b43e7"><strong>tests/test_adapters.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">textwrap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dedent</span></span>
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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;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Adapter</span><span class="p">,</span> <span class="n" style="color: #333;">Match</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">AdapterSpecification</span><span class="p">)</span></span>
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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;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Adapter</span><span class="p">,</span> <span class="n" style="color: #333;">Match</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span></span>
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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>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_52</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">@@ -65,27 +63,6 @@ def test_str():</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_to</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</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;">'seq'</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;">'TTACGT'</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_expand_braces</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">expand_braces</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{0}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{1}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{2}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'AA'</span></span>
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75
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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="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{2}C'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'AAC'</span></span>
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76
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{3}TGACCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNTGACCC'</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{10}TGACCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNNNNNNNNTGACCC'</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{3}TGA{4}CCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNTGAAAACCC'</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{0}TGA{4}CCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTTGAAAACCC'</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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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;">test_expand_braces_fail</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expression</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'{'</span><span class="p">,</span> <span class="s" style="color: #d14;">'}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{1}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{-7}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N{7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AN{7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{4{}'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="s" style="color: #d14;">'A{4}{3}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{b}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{6X}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{X6}'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">expression</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python"></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_adapter</span><span class="p">():</span></span>
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90
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'AAAA'</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">)</span></span>
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91
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Adapter</span><span class="p">(</span><span class="s" style="color: #d14;">'TTTT'</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</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">@@ -193,143 +170,6 @@ def test_issue_265():</td>
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193
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">la</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_to</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">3</span></span>
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194
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"></span>
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195
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_file_notation</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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197
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'adapters.fasta'</span><span class="p">))</span></span>
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198
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<pre style="margin: 0;">-<span id="LC198" 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;">tmp_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>
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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="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">""">first_name</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="s" style="color: #d14;"> ADAPTER1</span></span>
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="s" style="color: #d14;"> >second_name</span></span>
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="python"><span class="s" style="color: #d14;"> ADAPTER2</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC204" 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>
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205
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</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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207
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="python"></span>
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208
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="n" style="color: #333;">adapters</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="s" style="color: #d14;">'file:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">))</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="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;">adapters</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">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="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'first_name'</span></span>
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211
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">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="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ADAPTER1'</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapters</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'second_name'</span></span>
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213
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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;">adapters</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ADAPTER2'</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapters</span><span class="p">:</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.2</span></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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217
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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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_wildcards</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_wildcards</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indels</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_not_linked</span><span class="p">():</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" 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'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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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225
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<pre style="margin: 0;">-<span id="LC225" 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'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" 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'</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;">-<span id="LC227" 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'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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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228
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<pre style="margin: 0;">-<span id="LC228" 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;">'XXXA'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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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229
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<pre style="margin: 0;">-<span id="LC229" 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$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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230
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<pre style="margin: 0;">-<span id="LC230" 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;">'AXXXX'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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231
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<pre style="margin: 0;">-<span id="LC231" 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="LC232" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_parameters</span><span class="p">():</span></span>
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235
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_parameters</span></span>
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<pre style="margin: 0;">-<span id="LC236" 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;">'e=0.1'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.1</span><span class="p">}</span></span>
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237
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<pre style="margin: 0;">-<span id="LC237" 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;">'error_rate=0.1'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.1</span><span class="p">}</span></span>
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238
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<pre style="margin: 0;">-<span id="LC238" 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;">'o=5'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">5</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC239" 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;">'min_overlap=5'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">5</span><span class="p">}</span></span>
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240
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<pre style="margin: 0;">-<span id="LC240" 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;">'o=7; e=0.4'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.4</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'anywhere'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC242" 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;">'required'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC243" 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;">'optional'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'e=hallo'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">KeyError</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'bla=0.1'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'e='</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="python"></span>
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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_parse_with_parameters</span><span class="p">():</span></span>
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254
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"> <span class="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>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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="LC256" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</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="LC257" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTACGT; e=0.15'</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="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.15</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTAAAA; o=5; e=0.11'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.11</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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<pre style="margin: 0;">-<span id="LC264" class="line" lang="python"></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'thename=ACG;e=0.15 ... TGT;e=0.17'</span><span class="p">,</span> <span class="s" style="color: #d14;">'thename=ACG;e=0.15...TGT;e=0.17'</span><span class="p">):</span></span>
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266
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC267" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.15</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.17</span></span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC271" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC272" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"seq,req1,req2"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ACG...TGT"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ACG...TGT$"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"^ACG...TGT"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"^ACG...TGT$"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anchoring_makes_front_linked_adapter_required</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">req1</span><span class="p">,</span> <span class="n" style="color: #333;">req2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC279" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a X...Y</span></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC281" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req1</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req2</span></span>
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<pre style="margin: 0;">-<span id="LC284" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC285" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"r1,r2,req1,req2"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC287" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</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>
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<pre style="margin: 0;">-<span id="LC289" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</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="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC291" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC292" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC293" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_adapter_back_required_optional</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">req1</span><span class="p">,</span> <span class="n" style="color: #333;">req2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC296" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a X...Y</span></span>
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<pre style="margin: 0;">-<span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">"ACG"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"...TGT"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC298" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req1</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req2</span></span>
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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC302" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"r1,r2,exp1,exp2"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</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="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</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="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC308" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC312" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_adapter_front_required_optional</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">exp1</span><span class="p">,</span> <span class="n" style="color: #333;">exp2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g X...Y</span></span>
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314
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">"ACG"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"...TGT"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r2</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="LC315" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">exp1</span></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">exp2</span></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anywhere_parameter</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC321" 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 class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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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322
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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323
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<pre style="margin: 0;">-<span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">adapter</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="s" style="color: #d14;">'CTGAAGTGAAGTACACGGTT;anywhere'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'suffix'</span></span>
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325
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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326
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<pre style="margin: 0;">-<span id="LC326" 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;">'foo1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGAAGTACACGGTTAAAAAAAAAA'</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;">-<span id="LC327" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterCutter</span></span>
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328
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p">[])</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"></span>
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333
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</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="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUFFIX</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_indels_empty_read</span><span class="p">(</span><span class="n" style="color: #333;">where</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Issue #376</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#83ff0d8e113228f36b352922cbbb938d0aa9384b"><strong>tests/test_commandline.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">@@ -98,10 +98,15 @@ def test_minimum_length(run):</td>
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<pre style="margin: 0;"> <span id="LC98" 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>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC101" 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>
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<pre style="margin: 0;">+<span id="LC101" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="s" style="color: #d14;">"""--too-short-output"""</span></span>
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<pre style="margin: 0;"> <span id="LC103" 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="o" style="font-weight: 600;">.</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>
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104
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<pre style="margin: 0;">-<span id="LC104" 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 --too-short-output "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">too_short_path</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>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">([</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"> <span class="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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106
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<pre style="margin: 0;">+<span id="LC106" 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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="s" style="color: #d14;">"--too-short-output"</span><span class="p">,</span> <span class="n" style="color: #333;">too_short_path</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <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>
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<pre style="margin: 0;"> <span id="LC110" 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;">'tooshort.fa'</span><span class="p">),</span> <span class="n" style="color: #333;">too_short_path</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC112" 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">@@ -110,10 +115,15 @@ def test_maximum_length(run):</td>
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<pre style="margin: 0;"> <span id="LC115" 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>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC113" 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;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC118" 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;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"""--too-long-output"""</span></span>
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<pre style="margin: 0;"> <span id="LC120" 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;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'toolong.fa'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC116" 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 --too-long-output "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">too_long_path</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>
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<pre style="margin: 0;">+<span id="LC121" 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="LC122" 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="LC123" 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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<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;">"TTAGACATATCTCCGTCG"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="s" style="color: #d14;">"--too-long-output"</span><span class="p">,</span> <span class="n" style="color: #333;">too_long_path</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <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>
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<pre style="margin: 0;"> <span id="LC127" 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;">'toolong.fa'</span><span class="p">),</span> <span class="n" style="color: #333;">too_long_path</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC129" 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">@@ -394,9 +404,10 @@ def test_unconditional_cut_both(run):</td>
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394
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-u -5 -u 5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'unconditional-both.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)</span></span>
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395
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"></span>
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396
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC397" 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;">tmpdir</span><span class="p">):</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" 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;"><span class="idiff left">cores</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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398
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408
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<pre style="margin: 0;"> <span id="LC408" 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;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"untrimmed.fastq"</span><span class="p">))</span></span>
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399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">run</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 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>
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<pre style="margin: 0;">+<span id="LC409" 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>
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<pre style="margin: 0;">+<span id="LC410" 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>
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411
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<pre style="margin: 0;"> <span id="LC411" 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>
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412
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC413" 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">@@ -666,3 +677,8 @@ def test_force_fasta_output(tmpdir, cores):</td>
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_empty_read_with_wildcard_in_adapter</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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668
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679
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<pre style="margin: 0;"> <span id="LC679" 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>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="python"></span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"></span>
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682
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<pre style="margin: 0;">+<span id="LC682" 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;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">mocker</span><span class="p">):</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">mocker</span><span class="o" style="font-weight: 600;">.</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isatty</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">+<span id="LC684" 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;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"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>
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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.path</span></span>
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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;">shutil</span></span>
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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;">tempfile</span></span>
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<pre style="margin: 0;"> <span id="LC3" 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>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></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;">pytest</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">@@ -352,29 +351,31 @@ def test_pair_filter_first(run_paired, cores):</td>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC355" 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_paired_output</span><span class="p">(</span><span class="n" style="color: #333;">run_paired</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC354" 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_paired_output</span><span class="p">(</span><span class="n" style="color: #333;">run_paired</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"too-short.1.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"too-short.2.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"> <span class="n" style="color: #333;">run_paired</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="s" style="color: #d14;">"-a TTAGACATAT -A CAGTGGAGTA -m 14 --too-short-output "</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">"{0} --too-short-paired-output {1}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="s" style="color: #d14;">" -a TTAGACATAT -A CAGTGGAGTA -m 14"</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"> <span class="s" style="color: #d14;">" --too-short-output {}"</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="python"> <span class="s" style="color: #d14;">" --too-short-paired-output {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">in1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">,</span> <span class="n" style="color: #333;">in2</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">expected1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">,</span> <span class="n" style="color: #333;">expected2</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC363" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC363" 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;"><span class="idiff left right">cores</span></span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC365" 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;">"paired-too-short.1.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="n" style="color: #333;">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;">"paired-too-short.2.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">p2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"></span>
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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_too_long_output</span><span class="p">(</span><span class="n" style="color: #333;">run_paired</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC369" 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_output</span><span class="p">(</span><span class="n" style="color: #333;">run_paired</span><span class="p">,</span> <span class="n" style="color: #333;">tmpdir</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">cores</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"too-long.1.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"too-long.2.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">run_paired</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"> <span class="s" style="color: #d14;">"-a TTAGACATAT -A CAGTGGAGTA -M 14 --too-long-output "</span></span>
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="python"> <span class="s" style="color: #d14;">"{0} --too-long-paired-output {1}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="s" style="color: #d14;">" -a TTAGACATAT -A CAGTGGAGTA -M 14"</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="python"> <span class="s" style="color: #d14;">" --too-long-output {}"</span></span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">" --too-long-paired-output {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"> <span class="n" style="color: #333;">in1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">,</span> <span class="n" style="color: #333;">in2</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">expected1</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired-too-short.1.fastq"</span><span class="p">,</span> <span class="n" style="color: #333;">expected2</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"paired-too-short.2.fastq"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;"><span class="idiff left right">1</span></span></span>
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<pre style="margin: 0;">+<span id="LC378" 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;"><span class="idiff left right">cores</span></span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC380" 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;">"paired.1.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">p1</span><span class="p">)</span></span>
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381
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<pre style="margin: 0;"> <span id="LC381" 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;">"paired.2.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">p2</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">@@ -522,3 +523,15 @@ def test_combinatorial_demultiplexing(tmpdir):</td>
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<pre style="margin: 0;"> <span id="LC523" 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;">cutpath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial"</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="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Output file missing"</span></span>
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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</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;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</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="LC526" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC528" 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;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="python"> <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"info.txt"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC530" 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>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC532" 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;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.1.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="s" style="color: #d14;">"-p"</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.2.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC534" 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>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</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 class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/commit/ba3c2a62dda8394ca16835bfc2bf6b60bc3da4fc#9627b71ff9952493fda5865aea912319edd1cdd2"><strong>tests/test_parser.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">textwrap</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">dedent</span></span>
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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;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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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;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Adapter</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.parser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterSpecification</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_expand_braces</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">expand_braces</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{0}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{1}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{2}'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'AA'</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'A{2}C'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'AAC'</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{3}TGACCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNTGACCC'</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{10}TGACCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNNNNNNNNTGACCC'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{3}TGA{4}CCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTNNNTGAAAACCC'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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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;">expand_braces</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTN{0}TGA{4}CCC'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ACGTTGAAAACCC'</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_expand_braces_fail</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">expression</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'{'</span><span class="p">,</span> <span class="s" style="color: #d14;">'}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'{1}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{-7}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'N{7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AN{7'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{4{}'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'A{4}{3}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{b}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{6X}'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A{X6}'</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">expand_braces</span><span class="p">(</span><span class="n" style="color: #333;">expression</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_file_notation</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">'adapters.fasta'</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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;">tmp_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>
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<pre style="margin: 0;">+<span id="LC33" 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;">write</span><span class="p">(</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">""">first_name</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;"> ADAPTER1</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> >second_name</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> ADAPTER2</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> """</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC38" 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>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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="LC40" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</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="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;">adapters</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="s" style="color: #d14;">'file:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">cmdline_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'back'</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC43" 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;">adapters</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">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="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'first_name'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">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="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ADAPTER1'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapters</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'second_name'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapters</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'ADAPTER2'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapters</span><span class="p">:</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.2</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_wildcards</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_wildcards</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indels</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_not_linked</span><span class="p">():</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" 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'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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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<td class="diff-line-num new new_line" 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">
59
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<pre style="margin: 0;">+<span id="LC59" 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'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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">
60
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<pre style="margin: 0;">+<span id="LC60" 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'</span><span class="p">,</span> <span class="s" style="color: #d14;">'anywhere'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'anywhere'</span><span class="p">)</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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="LC62" 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;">'XXXA'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</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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63
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<pre style="margin: 0;">+<span id="LC63" 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$'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'anchored'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
64
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<pre style="margin: 0;">+<span id="LC64" 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;">'AXXXX'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</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="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">'noninternal'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A'</span><span class="p">,</span> <span class="p">{},</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" 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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_parameters</span><span class="p">():</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterSpecification</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse_parameters</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" 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;">'e=0.1'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.1</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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">
71
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<pre style="margin: 0;">+<span id="LC71" 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;">'error_rate=0.1'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.1</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" 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">
72
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<pre style="margin: 0;">+<span id="LC72" 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;">'o=5'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">5</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" 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;">'min_overlap=5'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">5</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
74
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<pre style="margin: 0;">+<span id="LC74" 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;">'o=7; e=0.4'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'min_overlap'</span><span class="p">:</span> <span class="mi" style="color: #099;">7</span><span class="p">,</span> <span class="s" style="color: #d14;">'max_error_rate'</span><span class="p">:</span> <span class="mf" style="color: #099;">0.4</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
75
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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="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'anywhere'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'anywhere'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
76
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<pre style="margin: 0;">+<span id="LC76" 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;">'required'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" 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;">'optional'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="s" style="color: #d14;">'required'</span><span class="p">:</span> <span class="bp" style="color: #999;">False</span><span class="p">}</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></span>
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79
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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="o" style="font-weight: 600;">.</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>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'e=hallo'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">KeyError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'bla=0.1'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</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>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">p</span><span class="p">(</span><span class="s" style="color: #d14;">'e='</span><span class="p">)</span></span>
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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>
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87
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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_parse_with_parameters</span><span class="p">():</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" 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>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</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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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTACGT; e=0.15'</span><span class="p">,</span> <span class="s" style="color: #d14;">'front'</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.15</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGTAAAA; o=5; e=0.11'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.11</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_overlap</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">5</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">spec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'thename=ACG;e=0.15 ... TGT;e=0.17'</span><span class="p">,</span> <span class="s" style="color: #d14;">'thename=ACG;e=0.15...TGT;e=0.17'</span><span class="p">):</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">spec</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.15</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.17</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"seq,req1,req2"</span><span class="p">,</span> <span class="p">[</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ACG...TGT"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ACG...TGT$"</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>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"^ACG...TGT"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"^ACG...TGT$"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"><span class="p">])</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anchoring_makes_front_linked_adapter_required</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">req1</span><span class="p">,</span> <span class="n" style="color: #333;">req2</span><span class="p">):</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a X...Y</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">)</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req1</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req2</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"r1,r2,req1,req2"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</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>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</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="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"><span class="p">])</span></span>
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129
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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_linked_adapter_back_required_optional</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">req1</span><span class="p">,</span> <span class="n" style="color: #333;">req2</span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -a X...Y</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">"ACG"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"...TGT"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="s" style="color: #d14;">"back"</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req1</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">req2</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"r1,r2,exp1,exp2"</span><span class="p">,</span> <span class="p">[</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</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="bp" style="color: #999;">True</span><span class="p">),</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</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="bp" style="color: #999;">True</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="s" style="color: #d14;">";required"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</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>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="s" style="color: #d14;">";optional"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="p">])</span></span>
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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_linked_adapter_front_required_optional</span><span class="p">(</span><span class="n" style="color: #333;">r1</span><span class="p">,</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="n" style="color: #333;">exp1</span><span class="p">,</span> <span class="n" style="color: #333;">exp2</span><span class="p">):</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># -g X...Y</span></span>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">"ACG"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r1</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"...TGT"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">r2</span><span class="p">,</span> <span class="s" style="color: #d14;">"front"</span><span class="p">)</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">exp1</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_required</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">exp2</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_adapter_parameters</span><span class="p">():</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># issue #394</span></span>
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<td class="diff-line-num new new_line" 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="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">(</span><span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.17</span><span class="p">,</span> <span class="n" style="color: #333;">indels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_parse</span><span class="p">(</span><span class="s" style="color: #d14;">"ACG...TGT"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
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<pre style="margin: 0;">+<span id="LC157" 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;">a</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.17</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_error_rate</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.17</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">front_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indels</span></span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back_adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">indels</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anywhere_parameter</span><span class="p">():</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" 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 class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">read_wildcards</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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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">adapter_wildcards</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;">indels</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">adapter</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;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="s" style="color: #d14;">'CTGAAGTGAAGTACACGGTT;anywhere'</span><span class="p">,</span> <span class="s" style="color: #d14;">'back'</span><span class="p">))[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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168
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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;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">remove</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'suffix'</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ANYWHERE</span></span>
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170
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<pre style="margin: 0;">+<span id="LC170" 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;">'foo1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGAAGTACACGGTTAAAAAAAAAA'</span><span class="p">)</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterCutter</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">])</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p">[])</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span></pre>
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