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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cutadapt">Debian Med / python-cutadapt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf">02bef8f8</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-12T18:36:06+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 3.1</pre>
</li>
</ul>
<h4>21 changed files:</h4>
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<li class="file-stats">
<a href="#d94622672672a69390631d825d55c7582120624e">
.codecov.yml
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<li class="file-stats">
<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">
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.github/workflows/ci.yml
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
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−
.travis.yml
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<li class="file-stats">
<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">
CHANGES.rst
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<li class="file-stats">
<a href="#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">
buildwheels.sh
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<li class="file-stats">
<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">
doc/guide.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="#8fb347891ec0a40b16ef2bdbe361f823e12aa016">
src/cutadapt/adapters.py
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<a href="#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae">
src/cutadapt/log.py
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<a href="#a44086ebe255bc0df91ea1d82811c828e6f5e324">
src/cutadapt/modifiers.py
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<li class="file-stats">
<a href="#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5">
src/cutadapt/parser.py
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<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">
src/cutadapt/pipeline.py
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<a href="#0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de">
src/cutadapt/report.py
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<a href="#af95dfcb30a51908f338d0fd6a196b9e4c108046">
src/cutadapt/utils.py
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tests/cut/action_retain.fasta
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tests/data/action_retain.fasta
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tests/test_command.py
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<a href="#83ff0d8e113228f36b352922cbbb938d0aa9384b">
tests/test_commandline.py
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<a href="#aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda">
tests/test_modifiers.py
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<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
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<h4>Changes:</h4>
<li id="d94622672672a69390631d825d55c7582120624e">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#d94622672672a69390631d825d55c7582120624e"><strong>.codecov.yml</strong></a>
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1
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">comment</span><span class="pi">:</span> <span class="s" style="color: #d14;">off</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2
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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">codecov</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">require_ci_to_pass</span><span class="pi">:</span> <span class="s" style="color: #d14;">no</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
</pre>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +7,11 @@ coverage:</td>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">range</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">90...100"</span></span>
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<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
10
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">status</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">project</span><span class="pi">:</span> <span class="s" style="color: #d14;">yes</span></span>
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<td class="diff-line-num new old_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">
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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="yaml"> <span class="na" style="color: #008080;">project</span><span class="pi">:</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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">default</span><span class="pi">:</span></span>
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<td class="diff-line-num new old_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">
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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="yaml"> <span class="na" style="color: #008080;">target</span><span class="pi">:</span> <span class="s" style="color: #d14;">auto</span></span>
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<td class="diff-line-num new old_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">
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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="yaml"> <span class="na" style="color: #008080;">threshold</span><span class="pi">:</span> <span class="s" style="color: #d14;">1%</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="yaml"> <span class="na" style="color: #008080;">base</span><span class="pi">:</span> <span class="s" style="color: #d14;">auto</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">patch</span><span class="pi">:</span> <span class="s" style="color: #d14;">no</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">changes</span><span class="pi">:</span> <span class="s" style="color: #d14;">no</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"></span>
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<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">CI</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">push</span><span class="pi">,</span> <span class="nv" style="color: #008080;">pull_request</span><span class="pi">]</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">lint</span><span class="pi">:</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;">5</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.7</span><span class="pi">]</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">toxenv</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">flake8</span><span class="pi">,</span> <span class="nv" style="color: #008080;">mypy</span><span class="pi">,</span> <span class="nv" style="color: #008080;">docs</span><span class="pi">]</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install dependencies</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="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install tox</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run tox ${{ matrix.toxenv }}</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tox -e ${{ matrix.toxenv }}</span></span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;">5</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-latest</span><span class="pi">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.9</span><span class="pi">]</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">macos-latest</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install dependencies</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install tox</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</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">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">tox -e py</span></span>
</pre>
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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="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Upload coverage report</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="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">codecov/codecov-action@v1</span></span>
</pre>
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<td class="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="yaml"></span>
</pre>
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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="yaml"> <span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">timeout-minutes</span><span class="pi">:</span> <span class="m" style="color: #099;">5</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">lint</span><span class="pi">,</span> <span class="nv" style="color: #008080;">test</span><span class="pi">]</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">startsWith(github.ref, 'refs/tags')</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">fetch-depth</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># required for setuptools_scm</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Make distributions</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install Cython</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="s" style="color: #d14;">python setup.py sdist</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="s" style="color: #d14;">./buildwheels.sh</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -l dist/</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Publish to PyPI</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypa/gh-action-pypi-publish@v1.4.1</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">__token__</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.pypi_password }}</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;">#password: ${{ secrets.test_pypi_password }}</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;">#repository_url: https://test.pypi.org/legacy/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">cache</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">directories</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">$HOME/.cache/pip</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install tox</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tox</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install codecov</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">codecov</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">global</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;">#- TWINE_REPOSITORY_URL=https://test.pypi.org/legacy/</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">TWINE_USERNAME=marcelm</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># TWINE_PASSWORD is set in Travis settings</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py36</span></span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"></span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py37</span></span>
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30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"></span>
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<td class="diff-line-num old old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>
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32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py38</span></span>
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33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"></span>
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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.9"</span></span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py39</span></span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"></span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">flake8</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=flake8</span></span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="yaml"></span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">mypy</span></span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=mypy</span></span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"></span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs</span></span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=docs</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">stage</span><span class="pi">:</span> <span class="s" style="color: #d14;">deploy</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">services</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">docker</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">install</span><span class="pi">:</span> <span class="s" style="color: #d14;">python3 -m pip install Cython twine</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">tag IS present</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 setup.py sdist</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml"> <span class="s" style="color: #d14;">./buildwheels.sh</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml"> <span class="s" style="color: #d14;">ls -l dist/</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml"> <span class="s" style="color: #d14;">python3 -m twine upload dist/*</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">allow_failures</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">nightly"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#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 +2,25 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"><span class="n" style="color: #333;">Changes</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"><span class="p">=======</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"><span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.1</span> <span class="p">(</span><span class="m" style="color: #099;">2020</span><span class="p">-</span><span class="m" style="color: #099;">12</span><span class="p">-</span><span class="m" style="color: #099;">03</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"><span class="p">-----------------</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">443</span><span class="p">`:</span> <span class="k" style="font-weight: 600;">With</span> <span class="p">``--</span><span class="n" style="color: #333;">action</span><span class="p">=</span><span class="n" style="color: #333;">retain</span><span class="p">``,</span> <span class="n" style="color: #333;">it</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">possible</span> <span class="k" style="font-weight: 600;">to</span> <span class="nf" style="color: #900; font-weight: 600;">trim</span> <span class="n" style="color: #333;">reads</span> <span class="k" style="font-weight: 600;">while</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">leaving</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">adapter</span> <span class="n" style="color: #333;">sequence</span> <span class="n" style="color: #333;">itself</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="nb" style="color: #0086b3;">read</span><span class="p">.</span> <span class="n" style="color: #333;">That</span> <span class="n" style="color: #333;">is</span><span class="p">,</span> <span class="n" style="color: #333;">only</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">before</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="m" style="color: #099;">5</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">’</span> <span class="n" style="color: #333;">adapters</span><span class="p">)</span> <span class="k" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">after</span> <span class="p">(</span><span class="n" style="color: #333;">for</span> <span class="m" style="color: #099;">3</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">’</span> <span class="n" style="color: #333;">adapters</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">removed</span><span class="p">.</span> <span class="k" style="font-weight: 600;">With</span> <span class="n" style="color: #333;">linked</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">both</span> <span class="n" style="color: #333;">adapters</span> <span class="n" style="color: #333;">are</span> <span class="n" style="color: #333;">retained</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">495</span><span class="p">`:</span> <span class="n" style="color: #333;">Running</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">multiple</span> <span class="n" style="color: #333;">cores</span> <span class="n" style="color: #333;">did</span> <span class="k" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">work</span> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">macOS</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">Python</span> <span class="m" style="color: #099;">3.8</span><span class="p">+.</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">
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">To</span> <span class="n" style="color: #333;">prevent</span> <span class="n" style="color: #333;">problems</span> <span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">these</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">future</span><span class="p">,</span> <span class="n" style="color: #333;">automated</span> <span class="n" style="color: #333;">testing</span> <span class="n" style="color: #333;">has</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">extended</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">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">also</span> <span class="nf" style="color: #900; font-weight: 600;">run</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">macOS</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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;">482</span><span class="p">`:</span> <span class="n" style="color: #333;">Print</span> <span class="n" style="color: #333;">statistics</span> <span class="n" style="color: #333;">for</span> <span class="p">``--</span><span class="n" style="color: #333;">discard</span><span class="p">-</span><span class="n" style="color: #333;">casava</span><span class="p">``</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">``--</span><span class="k" style="font-weight: 600;">max</span><span class="p">-</span><span class="n" style="color: #333;">ee</span><span class="p">``</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">the</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">report</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC17" 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;">497</span><span class="p">`:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">changelog</span> <span class="n" style="color: #333;">for</span> <span class="m" style="color: #099;">3.0</span> <span class="n" style="color: #333;">previously</span> <span class="n" style="color: #333;">forgot</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">mention</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">following</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">options</span><span class="p">,</span> <span class="n" style="color: #333;">which</span> <span class="n" style="color: #333;">were</span> <span class="n" style="color: #333;">deprecated</span> <span class="k" style="font-weight: 600;">in</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2.0</span><span class="p">,</span> <span class="n" style="color: #333;">have</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">been</span> <span class="n" style="color: #333;">removed</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</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">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"> <span class="n" style="color: #333;">using</span> <span class="n" style="color: #333;">them</span> <span class="n" style="color: #333;">will</span> <span class="n" style="color: #333;">lead</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">an</span> <span class="n" style="color: #333;">error</span><span class="p">:</span> <span class="p">``--</span><span class="n" style="color: #333;">format</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">colorspace</span><span class="p">``,</span> <span class="p">``-</span><span class="n" style="color: #333;">c</span><span class="p">``,</span> <span class="p">``-</span><span class="n" style="color: #333;">d</span><span class="p">``,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"> <span class="p">``--</span><span class="n" style="color: #333;">double</span><span class="p">-</span><span class="n" style="color: #333;">encode</span><span class="p">``,</span> <span class="p">``-</span><span class="n" style="color: #333;">t</span><span class="p">``,</span> <span class="p">``--</span><span class="nf" style="color: #900; font-weight: 600;">trim</span><span class="p">-</span><span class="n" style="color: #333;">primer</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">strip</span><span class="p">-</span><span class="n" style="color: #333;">f3</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">maq</span><span class="p">``,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="p">``--</span><span class="n" style="color: #333;">bwa</span><span class="p">``,</span> <span class="p">``--</span><span class="n" style="color: #333;">no</span><span class="p">-</span><span class="n" style="color: #333;">zero</span><span class="p">-</span><span class="n" style="color: #333;">cap</span><span class="p">``.</span> <span class="n" style="color: #333;">This</span> <span class="n" style="color: #333;">frees</span> <span class="n" style="color: #333;">up</span> <span class="n" style="color: #333;">some</span> <span class="n" style="color: #333;">single</span><span class="p">-</span><span class="n" style="color: #333;">character</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> <span class="n" style="color: #333;">allowing</span> <span class="n" style="color: #333;">them</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">be</span> <span class="n" style="color: #333;">re</span><span class="p">-</span><span class="n" style="color: #333;">purposed</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">future</span> <span class="n" style="color: #333;">Cutadapt</span> <span class="n" style="color: #333;">features</span><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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5
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"><span class="n" style="color: #333;">v3</span><span class="m" style="color: #099;">.0</span> <span class="p">(</span><span class="m" style="color: #099;">2020</span><span class="p">-</span><span class="m" style="color: #099;">11</span><span class="p">-</span><span class="m" style="color: #099;">10</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"><span class="p">-----------------</span></span>
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7
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +47,12 @@ v3.0 (2020-11-10)</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="mosel"><span class="s1" style="color: #d14;"> or had too many ``N``. (This unintentionally disappeared in a previous version.)</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="mosel"><span class="s1" style="color: #d14;">* :issue:`487`: When demultiplexing, the reported number of written pairs was</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="mosel"><span class="s1" style="color: #d14;"> always zero.</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="mosel"><span class="s1" style="color: #d14;">* :issue:`497`: The following options, which were deprecated in version 2.0, have</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="mosel"><span class="s1" style="color: #d14;"> been removed, and using them will lead to an error:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ``--format``, ``--colorspace``, ``-c``, ``-d``, ``--double-encode``,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ``-t``, ``--trim-primer``, ``--strip-f3``, ``--maq``, ``--bwa``, ``--no-zero-cap``.</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="mosel"><span class="s1" style="color: #d14;"> This frees up some single-character options,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="mosel"><span class="s1" style="color: #d14;"> allowing them to be re-purposed for future Cutadapt features.</span></span>
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31
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Ensure Cutadapt runs under Python 3.9.</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="mosel"><span class="s1" style="color: #d14;">* Drop support for Python 3.5.</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="mosel"></span>
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<li id="f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#f75f54159d8ca95918e0cdbdcbc2012a7f8d47ed"><strong>buildwheels.sh</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">@@ -16,7 +16,7 @@ manylinux=quay.io/pypa/manylinux2010_x86_64</td>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># For convenience, if this script is called from outside of a docker container,</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># it starts a container and runs itself inside of it.</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> docker /proc/1/cgroup<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">!</span> <span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: #000080;">-q</span> docker /proc/1/cgroup<span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">test</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-d</span></span><span class="idiff right"> /opt/python</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># We are not inside a container</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"> docker pull <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">manylinux</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">exec </span>docker run <span class="nt" style="color: #000080;">--rm</span> <span class="nt" style="color: #000080;">-v</span> <span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">pwd</span><span class="si" style="color: #d14;">)</span>:/io <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">manylinux</span><span class="k" style="font-weight: 600;">}</span> /io/<span class="nv" style="color: #008080;">$0</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -903,25 +903,47 @@ This section describes in which ways reads can be modified other than adapter</td>
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<pre style="margin: 0;"> <span id="LC903" class="line" lang="plaintext">removal.</span>
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<pre style="margin: 0;"> <span id="LC904" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC905" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC906" class="line" lang="plaintext"><span class="idiff left right">Not trimming adapters</span></span>
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<pre style="margin: 0;">-<span id="LC907" class="line" lang="plaintext"><span class="idiff left right">---------------------</span></span>
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="plaintext"><span class="idiff left right">.. _changing-what-is-done-when-an-adapter-is-found:</span></span>
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="plaintext"><span class="idiff left right">.. _action:</span></span>
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC909" class="line" lang="plaintext"><span class="idiff left right">Instead of removing an adapter from a read, it is also possible to take other</span></span>
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<pre style="margin: 0;">-<span id="LC910" class="line" lang="plaintext"><span class="idiff left right">actions when an adapter is found by specifying the ``--action`` option.</span></span>
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="plaintext"><span class="idiff left right">``--action`` changes what is done when an adapter is found</span></span>
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="plaintext"><span class="idiff left right">----------------------------------------------------------</span></span>
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC912" class="line" lang="plaintext">The <span class="idiff left right">default is ``--action=trim``, which will remove the adapter and either</span></span>
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<pre style="margin: 0;">-<span id="LC913" class="line" lang="plaintext"><span class="idiff left right">the sequence before or after it from the</span> read.</span>
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="plaintext">The <span class="idiff left right">``--action`` option can be used to change what is done when an adapter match</span></span>
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="plaintext"><span class="idiff left right">is found in a</span> read.</span>
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<pre style="margin: 0;"> <span id="LC914" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC915" class="line" lang="plaintext">Use ``--action=none`` to not remove the adapter from the read. This is useful</span>
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<pre style="margin: 0;">-<span id="LC916" class="line" lang="plaintext">when combined with other options, such as ``--untrimmed-output``, which</span>
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<pre style="margin: 0;">-<span id="LC917" class="line" lang="plaintext">will redirect the reads without adapter to a different file. Other read</span>
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918
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<pre style="margin: 0;">-<span id="LC918" class="line" lang="plaintext">modification options (as listed below) may still change the read.</span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="plaintext">The default is ``--action=trim``, which will remove the adapter and the</span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="plaintext">sequence before or after it from the read. For 5' adapters, the adapter and</span>
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917
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<pre style="margin: 0;">+<span id="LC917" class="line" lang="plaintext">the sequence preceding it is removed. For 3' adapters, the adapter and the</span>
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918
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<pre style="margin: 0;">+<span id="LC918" class="line" lang="plaintext">sequence following it is removed. Since linked adapters are a combination of</span>
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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="plaintext">a 5' and 3' adapter, in effect only the sequence between the 5' and the 3'</span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="plaintext">adapter matches is kept.</span>
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919
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921
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<pre style="margin: 0;"> <span id="LC921" class="line" lang="plaintext"></span>
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920
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<pre style="margin: 0;">-<span id="LC920" class="line" lang="plaintext">Use ``--action=mask`` to write ``N`` characters to that parts of the read</span>
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921
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<pre style="margin: 0;">-<span id="LC921" class="line" lang="plaintext">that would otherwise have been removed .</span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="plaintext">With ``--action=retain``, the read is trimmed, but the adapter sequence itself</span>
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923
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<pre style="margin: 0;">+<span id="LC923" class="line" lang="plaintext">is not removed. Up- and downstream sequences are removed in the same way as</span>
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924
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<pre style="margin: 0;">+<span id="LC924" class="line" lang="plaintext">for the ``trim`` action. For linked adapters, both adapter sequences are kept.</span>
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922
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925
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="plaintext"></span>
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923
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<pre style="margin: 0;">-<span id="LC923" class="line" lang="plaintext">Use ``--action=lowercase`` to change to lowercase that part of the read that would otherwise</span>
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924
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<pre style="margin: 0;">-<span id="LC924" class="line" lang="plaintext">have been removed. The rest is converted to uppercase.</span>
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926
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<pre style="margin: 0;">+<span id="LC926" class="line" lang="plaintext">.. note::</span>
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927
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<pre style="margin: 0;">+<span id="LC927" class="line" lang="plaintext"> Because it is somewhat unclear what should happen, ``--action=retain`` can</span>
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928
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="plaintext"> at the moment not be combined with ``--times`` (multiple rounds of adapter</span>
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929
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="plaintext"> removal).</span>
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930
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="plaintext"></span>
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931
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<pre style="margin: 0;">+<span id="LC931" class="line" lang="plaintext">Use ``--action=none`` to not change the read even if there is a match.</span>
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932
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<pre style="margin: 0;">+<span id="LC932" class="line" lang="plaintext">This is useful because the statistics will still be updated as before</span>
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933
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<pre style="margin: 0;">+<span id="LC933" class="line" lang="plaintext">and because the read will still be considered "trimmed" for the read</span>
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934
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<pre style="margin: 0;">+<span id="LC934" class="line" lang="plaintext">filtering options. Combining this with ``--untrimmed-output``, for</span>
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935
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<pre style="margin: 0;">+<span id="LC935" class="line" lang="plaintext">example, can be used to copy reads without adapters to a different</span>
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<pre style="margin: 0;">+<span id="LC936" class="line" lang="plaintext">file. Other read modification options, if used, may still change</span>
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937
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<pre style="margin: 0;">+<span id="LC937" class="line" lang="plaintext">the read.</span>
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938
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<pre style="margin: 0;">+<span id="LC938" class="line" lang="plaintext"></span>
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939
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<pre style="margin: 0;">+<span id="LC939" class="line" lang="plaintext">Use ``--action=mask`` to write ``N`` characters to those parts of the read</span>
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940
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<pre style="margin: 0;">+<span id="LC940" class="line" lang="plaintext">that would otherwise have been removed.</span>
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941
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<pre style="margin: 0;">+<span id="LC941" class="line" lang="plaintext"></span>
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942
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<pre style="margin: 0;">+<span id="LC942" class="line" lang="plaintext">Use ``--action=lowercase`` to change to lowercase those parts of the read that</span>
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943
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<pre style="margin: 0;">+<span id="LC943" class="line" lang="plaintext">would otherwise have been removed. The rest is converted to uppercase.</span>
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944
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<pre style="margin: 0;">+<span id="LC944" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC945" class="line" lang="plaintext">.. versionadded:: 3.1</span>
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946
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<pre style="margin: 0;">+<span id="LC946" class="line" lang="plaintext"> The ``retain`` action.</span>
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925
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947
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<pre style="margin: 0;"> <span id="LC947" class="line" lang="plaintext"></span>
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926
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948
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<pre style="margin: 0;"> <span id="LC948" class="line" lang="plaintext"></span>
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927
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949
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<pre style="margin: 0;"> <span id="LC949" class="line" lang="plaintext">.. _cut-bases:</span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#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">@@ -92,6 +92,7 @@ setup(</td>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://cutadapt.readthedocs.io/'</span><span class="p">,</span></span>
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93
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'trim adapters from high-throughput sequencing reads'</span><span class="p">,</span></span>
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94
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</span><span class="p">,</span></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;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/x-rst'</span><span class="p">,</span></span>
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95
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'MIT'</span><span class="p">,</span></span>
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96
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'build_ext'</span><span class="p">:</span> <span class="n" style="color: #333;">BuildExt</span><span class="p">,</span> <span class="s" style="color: #d14;">'sdist'</span><span class="p">:</span> <span class="n" style="color: #333;">SDist</span><span class="p">},</span></span>
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97
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#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">@@ -125,9 +125,8 @@ def get_argument_parser() -> ArgumentParser:</td>
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Show this help message and exit"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--version"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Show version number and exit"</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="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">)</span></span>
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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="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--debug"</span><span class="p">,</span> <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"?"</span><span class="p">,</span> <span class="n" style="color: #333;">const</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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129
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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"trace"</span><span class="p">,</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="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Print debug log. 'trace' prints also DP matrices"</span><span class="p">)</span></span>
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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="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--debug"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"count"</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;">0</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Print debug log. Use twice to also print DP matrices"</span><span class="p">)</span></span>
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131
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--profile"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span> <span class="n" style="color: #333;">default</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;">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="LC131" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-j'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--cores'</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;">1</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="s" style="color: #d14;">'Number of CPU cores to use. Use 0 to auto-detect. Default: %(default)s'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -192,12 +191,14 @@ def get_argument_parser() -> ArgumentParser:</td>
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192
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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;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-N"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--no-match-adapter-wildcards"</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_false"</span><span class="p">,</span></span>
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193
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'match_adapter_wildcards'</span><span class="p">,</span></span>
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194
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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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Do not interpret IUPAC wildcards in adapters."</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="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--action"</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'trim'</span><span class="p">,</span> <span class="s" style="color: #d14;">'mask'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lowercase'</span><span class="p">,</span> <span class="s" style="color: #d14;">'none'</span><span class="p">),</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'trim'</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="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"What to do with found adapters. "</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;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--action"</span><span class="p">,</span> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"trim"</span><span class="p">,</span> <span class="s" style="color: #d14;">"retain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mask"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lowercase"</span><span class="p">,</span> <span class="s" style="color: #d14;">"none"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"trim"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"What to do if a match was found. "</span></span>
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="s" style="color: #d14;">"trim: trim adapter and up- or downstream sequence; "</span></span>
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="python"> <span class="s" style="color: #d14;">"retain: trim, but retain adapter; "</span></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">"mask: replace with 'N' characters; "</span></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;">"lowercase: convert to lowercase; "</span></span>
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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"> <span class="s" style="color: #d14;">"none: leave unchanged (useful with "</span></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="s" style="color: #d14;">"--discard-untrimmed). Default: %(default)s"</span><span class="p">)</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;">"none: leave unchanged. Default: %(default)s"</span><span class="p">)</span></span>
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201
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--rc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--revcomp"</span><span class="p">,</span> <span class="n" style="color: #333;">dest</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"reverse_complement"</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"store_true"</span><span class="p">,</span></span>
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203
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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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Check both the read and its reverse complement for adapter matches. If "</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -724,7 +725,7 @@ def adapters_from_args(args) -> Tuple[List[Adapter], List[Adapter]]:</td>
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724
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725
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<pre style="margin: 0;"> <span id="LC725" 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="n" style="color: #333;">e</span><span class="p">)</span></span>
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726
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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python"> <span class="n" style="color: #333;">warn_duplicate_adapters</span><span class="p">(</span><span class="n" style="color: #333;">adapters</span><span class="p">)</span></span>
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726
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727
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<pre style="margin: 0;"> <span id="LC727" class="line" lang="python"> <span class="n" style="color: #333;">warn_duplicate_adapters</span><span class="p">(</span><span class="n" style="color: #333;">adapters2</span><span class="p">)</span></span>
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727
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;"><span class="idiff left">==</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"trace"</span></span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span> <span class="o" style="font-weight: 600;"><span class="idiff left">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">:</span></span>
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729
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<pre style="margin: 0;"> <span id="LC729" 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="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">adapters2</span><span class="p">:</span></span>
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729
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span><span class="p">.</span><span class="n" style="color: #333;">enable_debug</span><span class="p">()</span></span>
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730
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">adapters2</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -776,10 +777,13 @@ def add_adapter_cutter(</td>
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776
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="p">.</span><span class="n" style="color: #333;">add_paired_modifier</span><span class="p">(</span><span class="n" style="color: #333;">cutter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC778" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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779
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="python"> <span class="n" style="color: #333;">adapter_cutter</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_cutter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span></span>
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779
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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapters</span><span class="p">:</span></span>
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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;">adapter_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;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">allow_index</span><span class="p">)</span></span>
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781
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapters2</span><span class="p">:</span></span>
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782
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">adapter_cutter2</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;">adapters2</span><span class="p">,</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">allow_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapters</span><span class="p">:</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"> <span class="n" style="color: #333;">adapter_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;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">allow_index</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapters2</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="python"> <span class="n" style="color: #333;">adapter_cutter2</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;">adapters2</span><span class="p">,</span> <span class="n" style="color: #333;">times</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">allow_index</span><span class="p">)</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</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="LC786" 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="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC787" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>
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784
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">:</span></span>
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785
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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;">raise</span> <span class="n" style="color: #333;">CommandLineError</span><span class="p">(</span><span class="s" style="color: #d14;">"--revcomp not implemented for paired-end reads"</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="837" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -837,11 +841,11 @@ def main(cmdlineargs, default_outfile=sys.stdout.buffer) -> Statistics:</td>
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841
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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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842
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<pre style="margin: 0;"> <span id="LC842" 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;">get_argument_parser</span><span class="p">()</span></span>
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">leftover_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_known_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmdlineargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC840" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># log to stderr if results are to be sent to stdout</span></span>
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<pre style="margin: 0;">-<span id="LC841" class="line" lang="python"> <span class="n" style="color: #333;">log_to_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">paired_output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span></span>
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842
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844
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<pre style="margin: 0;"> <span id="LC844" 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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843
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845
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<pre style="margin: 0;"> <span id="LC845" 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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844
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846
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<pre style="margin: 0;"> <span id="LC846" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">root</span><span class="p">.</span><span class="n" style="color: #333;">handlers</span><span class="p">:</span></span>
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847
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<pre style="margin: 0;">+<span id="LC847" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># If results are to be sent to stdout, logging needs to go to stderr</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"> <span class="n" style="color: #333;">log_to_stdout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">paired_output</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span></span>
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="python"> <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">log_to_stdout</span><span class="p">,</span></span>
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846
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850
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<pre style="margin: 0;"> <span id="LC850" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">quiet</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'minimal'</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">)</span></span>
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851
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<pre style="margin: 0;"> <span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">log_header</span><span class="p">(</span><span class="n" style="color: #333;">cmdlineargs</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#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">@@ -151,6 +151,10 @@ class Match(ABC):</td>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">remainder_interval</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;">Tuple</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></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="LC154" 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="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">retained_adapter_interval</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;">Tuple</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</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="n" style="color: #333;">abstractmethod</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_info_records</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="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">List</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</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">@@ -271,6 +275,9 @@ class RemoveBeforeMatch(SingleMatch):</td>
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271
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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272
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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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstop</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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273
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">retained_adapter_interval</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;">Tuple</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">]:</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstart</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">sequence</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>
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274
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trim_slice</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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275
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Same as remainder_interval, but as a slice() object</span></span>
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276
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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;">return</span> <span class="nb" style="color: #0086b3;">slice</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstop</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -306,6 +313,9 @@ class RemoveAfterMatch(SingleMatch):</td>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstart</span></span>
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">retained_adapter_interval</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;">Tuple</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</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;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstop</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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trim_slice</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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310
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Same as remainder_interval, but as a slice() object</span></span>
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311
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">slice</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">rstart</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -329,9 +339,7 @@ def _generate_adapter_name(_start=[1]) -> str:</td>
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329
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">name</span></span>
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330
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340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Adapter</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="LC333" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"adapter with one component"</span> <span class="c1" style="color: #998; font-style: italic;"># this is overriden in subclasses</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Matchable</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="LC343" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC344" 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="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="bp" style="color: #999;">self</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>
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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">@@ -345,6 +353,15 @@ class Adapter(ABC):</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"></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="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Adapter</span><span class="p">(</span><span class="n" style="color: #333;">Matchable</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="LC357" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"adapter with one component"</span> <span class="c1" style="color: #998; font-style: italic;"># this is overriden in subclasses</span></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC360" 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="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_statistics</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;">AdapterStatistics</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleAdapter</span><span class="p">(</span><span class="n" style="color: #333;">Adapter</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="LC366" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> This class can find a single adapter characterized by sequence, error rate,</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">@@ -685,6 +702,18 @@ class LinkedMatch(Match):</td>
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">match</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">front_match</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">back_match</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</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="LC703" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">remainder</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="LC704" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">retained_adapter_interval</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;">Tuple</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">front_match</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">front_match</span><span class="p">.</span><span class="n" style="color: #333;">rstart</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">front_match</span><span class="p">.</span><span class="n" style="color: #333;">rstop</span></span>
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<pre style="margin: 0;">+<span id="LC709" 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="LC710" class="line" lang="python"> <span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</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="LC711" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">back_match</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">back_match</span><span class="p">.</span><span class="n" style="color: #333;">rstop</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">offset</span></span>
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<pre style="margin: 0;">+<span id="LC713" 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="LC714" class="line" lang="python"> <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">front_match</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="LC715" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span></span>
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_info_records</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="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">List</span><span class="p">]:</span></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">records</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">namesuffix</span> <span class="ow" style="font-weight: 600;">in</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">@@ -707,11 +736,11 @@ class LinkedAdapter(Adapter):</td>
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<pre style="margin: 0;"> <span id="LC736" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC737" 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="LC738" 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="LC710" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC712" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="python"> <span class="n" style="color: #333;">front_adapter</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleAdapter</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC740" class="line" lang="python"> <span class="n" style="color: #333;">back_adapter</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">SingleAdapter</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="python"> <span class="n" style="color: #333;">front_required</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">bool</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"> <span class="n" style="color: #333;">back_required</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">bool</span></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;">name</span><span class="p"><span class="idiff left">:</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">str</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC744" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC745" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</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="LC746" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><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>
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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">@@ -754,11 +783,11 @@ class LinkedAdapter(Adapter):</td>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"></span>
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785
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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC757" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultipleAdapters</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Adapter</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MultipleAdapters</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Matchable</span></span><span class="p">):</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;">"""</span></span>
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759
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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;"> Represent multiple adapters at once</span></span>
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760
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC761" 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;">adapters</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">Adapter</span></span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC790" 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;">adapters</span><span class="p">:</span> <span class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">Matchable</span></span><span class="p">]):</span></span>
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</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;">"multiple_adapters"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapters</span></span>
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<pre style="margin: 0;"> <span id="LC793" 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">@@ -792,7 +821,7 @@ class MultipleAdapters(Adapter):</td>
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<pre style="margin: 0;"> <span id="LC821" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">best_match</span></span>
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<pre style="margin: 0;"> <span id="LC822" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC823" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC795" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">IndexedAdapters</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Adapter</span></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="LC824" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">IndexedAdapters</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">Matchable</span></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="LC825" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"><span class="s" style="color: #d14;"> Represent multiple adapters of the same type at once and use an index data structure</span></span>
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"><span class="s" style="color: #d14;"> to speed up matching. This acts like a "normal" Adapter as it provides a match_to</span></span>
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<li id="7107bed35fcb7c2440b754bf9d882e70c6ceb8ae">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#7107bed35fcb7c2440b754bf9d882e70c6ceb8ae"><strong>src/cutadapt/log.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">@@ -6,6 +6,17 @@ import logging</td>
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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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<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;">CrashingHandler</span><span class="p">(</span><span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">StreamHandler</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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">emit</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="LC12" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unlike the method it overrides, this will not catch exceptions"""</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nb" style="color: #0086b3;">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="LC14" class="line" lang="python"> <span class="n" style="color: #333;">stream</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">stream</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">stream</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">terminator</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</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>
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<pre style="margin: 0;"> <span id="LC20" 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="p">.</span><span class="n" style="color: #333;">Formatter</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC22" 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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +30,7 @@ class NiceFormatter(logging.Formatter):</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="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;"><span class="idiff left right">False</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">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="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;"> Attach handler to the global logger object</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,12 +39,10 @@ def setup_logging(logger, stdout=False, minimal=False, quiet=False, debug=False)</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># INFO level (and the ERROR level would give us an 'ERROR:' prefix).</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">addLevelName</span><span class="p">(</span><span class="n" style="color: #333;">REPORT</span><span class="p">,</span> <span class="s" style="color: #d14;">'REPORT'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="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="p">.</span><span class="n" style="color: #333;">StreamHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</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="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CrashingHandler</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">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="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">stream_handler</span><span class="p">.</span><span class="n" style="color: #333;">setFormatter</span><span class="p">(</span><span class="n" style="color: #333;">NiceFormatter</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># debug overrides quiet overrides minimal</span></span>
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<pre style="margin: 0;">-<span id="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="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">debug</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></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;">level</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span></span>
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<pre style="margin: 0;"> <span id="LC47" 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="LC48" 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="p">.</span><span class="n" style="color: #333;">ERROR</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#a44086ebe255bc0df91ea1d82811c828e6f5e324"><strong>src/cutadapt/modifiers.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,8 @@ from abc import ABC, abstractmethod</td>
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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;">OrderedDict</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 class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.qualtrim</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">quality_trim_index</span><span class="p">,</span> <span class="n" style="color: #333;">nextseq_trim_index</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleAdapters</span><span class="p">,</span> <span class="n" style="color: #333;">SingleAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedPrefixAdapters</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedSuffixAdapters</span><span class="p">,</span> <span class="n" style="color: #333;">Match</span><span class="p">,</span> <span class="n" style="color: #333;">remainder</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MultipleAdapters</span><span class="p">,</span> <span class="n" style="color: #333;">SingleAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedPrefixAdapters</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedSuffixAdapters</span><span class="p">,</span> \</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">Match</span><span class="p">,</span> <span class="n" style="color: #333;">remainder</span><span class="p">,</span> <span class="n" style="color: #333;">Adapter</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;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">reverse_complemented_sequence</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" 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">@@ -76,18 +77,23 @@ class AdapterCutter(SingleEndModifier):</td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span 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="LC79" 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="LC79" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span><span class="p">:</span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">Single</span>Adapter</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;">adapters</span><span class="p">:</span> <span class="n" style="color: #333;">List</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="LC81" class="line" lang="python"> <span class="n" style="color: #333;">times</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="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="LC82" class="line" lang="python"> <span class="n" style="color: #333;">action</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"trim"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC85" 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;"> action -- What to do with a found adapter: None, 'trim', 'mask' or 'lowercase'</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"><span class="s" style="color: #d14;"> action -- What to do with a found adapter:</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"><span class="s" style="color: #d14;"> None: Do nothing, only update the ModificationInfo appropriately</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"><span class="s" style="color: #d14;"> "trim": Remove the adapter and down- or upstream sequence depending on adapter type</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;"> "mask": Replace the part of the sequence that would have been removed with "N" bases</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;"> "lowercase": Convert the part of the sequence that would have been removed to lowercase</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> "retain": Like "trim", but leave the adapter sequence itself in the read</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;"> index -- if True, an adapter index (for multiple adapters) is created if possible</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">times</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">times</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">action</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">'trim'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'mask'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'lowercase'</span></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="LC96" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">action</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"trim"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"mask"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"lowercase"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"retain"</span></span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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91
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97
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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="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">action</span></span>
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98
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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="p">.</span><span class="n" style="color: #333;">with_adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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93
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99
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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="p">.</span><span class="n" style="color: #333;">adapter_statistics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">((</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="n" style="color: #333;">a</span><span class="p">.</span><span class="n" style="color: #333;">create_statistics</span><span class="p">())</span> <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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,6 +101,8 @@ class AdapterCutter(SingleEndModifier):</td>
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95
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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="p">.</span><span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MultipleAdapters</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_regroup_into_indexed_adapters</span><span class="p">(</span><span class="n" style="color: #333;">adapters</span><span class="p">))</span></span>
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96
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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;">else</span><span class="p">:</span></span>
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97
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MultipleAdapters</span><span class="p">(</span><span class="n" style="color: #333;">adapters</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;">if</span> <span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"retain"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">times</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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105
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<pre style="margin: 0;">+<span id="LC105" 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;">"'retain' cannot be combined with times > 1"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"></span>
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99
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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;">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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100
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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="s" style="color: #d14;">'AdapterCutter(adapters={!r}, times={}, action={!r})'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,6 +149,11 @@ class AdapterCutter(SingleEndModifier):</td>
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141
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149
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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142
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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;">return</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">suffix</span><span class="p">,</span> <span class="n" style="color: #333;">other</span></span>
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143
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" 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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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">trim_but_retain_adapter</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 class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;">Match</span><span class="p">]):</span></span>
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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;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</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="n" style="color: #333;">retained_adapter_interval</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span><span class="p">[</span><span class="n" style="color: #333;">start</span><span class="p">:</span><span class="n" style="color: #333;">stop</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>
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157
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<pre style="margin: 0;"> <span id="LC157" 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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145
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">masked_read</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 class="n" style="color: #333;">Sequence</span><span class="p">[</span><span class="n" style="color: #333;">Match</span><span class="p">]):</span></span>
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146
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159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">remainder</span><span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -174,7 +187,7 @@ class AdapterCutter(SingleEndModifier):</td>
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174
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match_and_trim</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>
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175
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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176
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"><span class="s" style="color: #d14;"> Search for the best-matching adapter in a read, perform the requested action</span></span>
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177
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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="s" style="color: #d14;"> ('trim', 'mask'<span class="idiff left right">, 'lowercase' or None</span> as determined by self.action) and return the</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"><span class="s" style="color: #d14;"> ('trim', 'mask'<span class="idiff left right"> etc.</span> as determined by self.action) and return the</span></span>
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178
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"><span class="s" style="color: #d14;"> (possibly) modified read.</span></span>
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179
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;"> *self.times* adapter removal rounds are done. During each round,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -184,7 +197,7 @@ class AdapterCutter(SingleEndModifier):</td>
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184
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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;"> Return a pair (trimmed_read, matches), where matches is a list of Match instances.</span></span>
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185
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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;"> """</span></span>
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186
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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;">matches</span> <span class="o" style="font-weight: 600;">=</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="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lowercase'</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 class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lowercase'</span><span class="p">:</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># TODO this should not be needed</span></span></span>
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188
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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;">read</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;">read</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span></span>
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189
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202
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<pre style="margin: 0;"> <span id="LC202" 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;">read</span></span>
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190
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203
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<pre style="margin: 0;"> <span id="LC203" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">times</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">@@ -201,12 +214,14 @@ class AdapterCutter(SingleEndModifier):</td>
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201
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'trim'</span><span class="p">:</span></span>
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202
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># read is already trimmed, nothing to do</span></span>
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203
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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;">pass</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;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'retain'</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">trim_but_retain_adapter</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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204
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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;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'mask'</span><span class="p">:</span></span>
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205
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">masked_read</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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206
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lowercase'</span><span class="p">:</span></span>
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207
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">lowercased_read</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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208
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223
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<pre style="margin: 0;"> <span id="LC223" 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;">trimmed_read</span><span class="p">.</span><span class="n" style="color: #333;">sequence</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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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># --no-trim</span></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;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</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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210
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225
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<pre style="margin: 0;"> <span id="LC225" 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;">read</span><span class="p">[:]</span></span>
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211
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"></span>
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212
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trimmed_read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="336" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -321,6 +336,8 @@ class PairedAdapterCutter(PairedModifier):</td>
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321
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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;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'lowercase'</span><span class="p">:</span></span>
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322
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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;">trimmed_read</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;">lowercased_read</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">match</span><span class="p">])</span></span>
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323
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338
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<pre style="margin: 0;"> <span id="LC338" 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;">trimmed_read</span><span class="p">.</span><span class="n" style="color: #333;">sequence</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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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'retain'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC340" 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;">AdapterCutter</span><span class="p">.</span><span class="n" style="color: #333;">trim_but_retain_adapter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">match</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">action</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># --no-trim</span></span>
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<pre style="margin: 0;"> <span id="LC342" 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;">read</span><span class="p">[:]</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">trimmed_read</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#12b6e14dcfabba52d86396a9e2818f75b0c0c8d5"><strong>src/cutadapt/parser.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -352,7 +352,7 @@ class AdapterParser:</td>
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<pre style="margin: 0;"> <span id="LC352" 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="LC353" 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="p">.</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="LC354" 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="p">.</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="LC355" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">n<span class="idiff left">ot</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">nam</span>e</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;">n<span class="idiff left">ame</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">is</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">Non</span>e</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;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">front_spec</span><span class="p">.</span><span class="n" style="color: #333;">name</span></span>
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC358" 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="p">.</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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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#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">@@ -4,7 +4,7 @@ import sys</td>
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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;">copy</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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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">functools</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;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">IO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">,</span> <span class="n" style="color: #333;">TextIO</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Dict</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;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">BinaryIO</span><span class="p">,</span> <span class="n" style="color: #333;">TextIO</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span><span class="p">,</span> <span class="n" style="color: #333;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Dict</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;">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="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">multiprocessing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Process</span><span class="p">,</span> <span class="n" style="color: #333;">Pipe</span><span class="p">,</span> <span class="n" style="color: #333;">Queue</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</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">@@ -120,7 +120,7 @@ class OutputFiles:</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">f</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">as_bytesio</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="LC123" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">as_bytesio</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"OutputFiles"</span></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;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;"> Create a new OutputFiles instance that has BytesIO instances for each non-None output file</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -141,6 +141,13 @@ class OutputFiles:</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="p">.</span><span class="n" style="color: #333;">demultiplex_out2</span><span class="p">[</span><span class="n" style="color: #333;">k</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="p">.</span><span class="n" style="color: #333;">BytesIO</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;">result</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span 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="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"""Close all output files that are not stdout"""</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">:</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="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python"></span>
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"></span>
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152
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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;">Pipeline</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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153
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<pre style="margin: 0;"> <span id="LC153" 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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -150,7 +157,6 @@ class Pipeline(ABC):</td>
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150
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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;">paired</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>
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152
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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;">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;">file_opener</span><span class="p">:</span> <span class="n" style="color: #333;">FileOpener</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC153" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[IO]</span></span>
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154
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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 class="c1" style="color: #998; font-style: italic;"># type: Any</span></span>
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155
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_filters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[Any]</span></span>
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156
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_infiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># type: Optional[InputFiles]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -168,7 +174,7 @@ class Pipeline(ABC):</td>
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168
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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169
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175
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>
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170
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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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<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;">connect_io</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">:</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">connect_io</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">:</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="bp" style="color: #999;">self</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;">infiles</span></span>
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173
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179
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">()</span></span>
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174
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -182,7 +188,7 @@ class Pipeline(ABC):</td>
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182
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="p">):</span></span>
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183
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</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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185
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<pre style="margin: 0;">-<span id="LC185" 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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191
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<pre style="margin: 0;">+<span id="LC191" 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 class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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186
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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187
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfiles</span></span>
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188
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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;">filter_wrapper</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_filter_wrapper</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">@@ -262,20 +268,21 @@ class Pipeline(ABC):</td>
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262
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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263
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span 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="LC271" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_input</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_close_output</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_close_input</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="bp" style="color: #999;">None</span><span class="p">:</span></span>
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265
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_infiles</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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267
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_infiles</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_close_output</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="bp" style="color: #999;">None</span><span class="p">:</span></span>
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268
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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;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_textiowrappers</span><span class="p">:</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># This also closes the underlying files; a second close occurs below</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Closing a TextIOWrapper also closes the underlying file, so</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># this closes some files a second time.</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</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="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="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="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO do not use hasattr</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'close'</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">outs</span> <span class="ow" style="font-weight: 600;">in</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;">demultiplex_out</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;">demultiplex_out2</span><span class="p">]:</span></span>
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<pre style="margin: 0;">-<span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">outs</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="LC277" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">out</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">outs</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="python"> <span class="n" style="color: #333;">out</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">uses_qualities</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="nb" style="color: #0086b3;">bool</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">@@ -283,7 +290,7 @@ class Pipeline(ABC):</td>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader</span><span class="p">.</span><span class="n" style="color: #333;">delivers_qualities</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC292" 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="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Optional</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"></span>
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296
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<pre style="margin: 0;"> <span id="LC296" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -316,7 +323,7 @@ class SingleEndPipeline(Pipeline):</td>
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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;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Modifier must not be None"</span><span class="p">)</span></span>
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317
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)</span></span>
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318
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"></span>
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319
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<pre style="margin: 0;">-<span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Optional</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>
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320
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="s" style="color: #d14;">"""Run the pipeline. Return statistics"""</span></span>
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321
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># no. of processed reads</span></span>
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322
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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;">total_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -402,7 +409,7 @@ class PairedEndPipeline(Pipeline):</td>
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402
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Whether to ignore pair_filter mode for discard-untrimmed filter</span></span>
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403
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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404
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC405" 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;">Optional</span><span class="p">[</span><span class="n" style="color: #333;">SingleEndModifier</span><span class="p">],</span> <span class="n" style="color: #333;">modifier2</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="n" style="color: #333;">SingleEndModifier</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 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;">Optional</span><span class="p">[</span><span class="n" style="color: #333;">SingleEndModifier</span><span class="p">],</span> <span class="n" style="color: #333;">modifier2</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="n" style="color: #333;">SingleEndModifier</span><span class="p">])</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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406
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413
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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407
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414
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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"><span class="s" style="color: #d14;"> Add a modifier for R1 and R2. One of them can be None, in which case the modifier</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"><span class="s" style="color: #d14;"> will only be added for the respective 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">@@ -411,18 +418,18 @@ class PairedEndPipeline(Pipeline):</td>
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<pre style="margin: 0;"> <span id="LC418" 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;">"Not both modifiers can be None"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">PairedModifierWrapper</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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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">:</span> <span class="n" style="color: #333;">SingleEndModifier</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">:</span> <span class="n" style="color: #333;">SingleEndModifier</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</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="s" style="color: #d14;"> Add one modifier for both R1 and R2</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">modifier</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="LC426" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">PairedModifierWrapper</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">,</span> <span class="n" style="color: #333;">copy</span><span class="p">.</span><span class="n" style="color: #333;">copy</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC421" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_paired_modifier</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">paired_modifier</span><span class="p">:</span> <span class="n" style="color: #333;">PairedModifier</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_paired_modifier</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">paired_modifier</span><span class="p">:</span> <span class="n" style="color: #333;">PairedModifier</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="s" style="color: #d14;">"""Add a Modifier (without wrapping it in a PairedModifierWrapper)"""</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">paired_modifier</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC425" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">progress</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;">None</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Tuple</span></span><span class="p"><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"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Optional</span></span><span class="p"><span class="idiff">[</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">]]</span>:</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># no. of processed reads</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="n" style="color: #333;">total1_bp</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="LC435" class="line" lang="python"> <span class="n" style="color: #333;">total2_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</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">@@ -594,8 +601,17 @@ class WorkerProcess(Process):</td>
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<pre style="margin: 0;"> <span id="LC601" 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="LC602" 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="LC603" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC597" 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;">two_input_files</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC598" 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="LC604" 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="LC605" 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="LC606" class="line" lang="python"> <span class="n" style="color: #333;">id_</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="p">:</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">two_input_files</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">interleaved_input</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python"> <span class="n" style="color: #333;">orig_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="LC611" class="line" lang="python"> <span class="n" style="color: #333;">read_pipe</span><span class="p">:</span> <span class="n" style="color: #333;">Connection</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="python"> <span class="n" style="color: #333;">write_pipe</span><span class="p">:</span> <span class="n" style="color: #333;">Connection</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="python"> <span class="n" style="color: #333;">need_work_queue</span><span class="p">:</span> <span class="n" style="color: #333;">Queue</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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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="p">.</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="LC617" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -604,7 +620,9 @@ class WorkerProcess(Process):</td>
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_write_pipe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">write_pipe</span></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_need_work_queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">need_work_queue</span></span>
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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="p">.</span><span class="n" style="color: #333;">_original_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="LC623" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Do not store orig_outfiles directly because it contains</span></span>
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># _io.BufferedWriter attributes, which cannot be pickled.</span></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_original_outfiles</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;">as_bytesio</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC626" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC627" 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="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</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">@@ -690,7 +708,7 @@ class PipelineRunner(ABC):</td>
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"><span class="s" style="color: #d14;"> A read processing pipeline</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC693" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__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;">progress</span><span class="p">:</span> <span class="n" style="color: #333;">Progress</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="n" style="color: #333;"><span class="idiff right">kwargs</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC711" 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;">progress</span><span class="p">:</span> <span class="n" style="color: #333;">Progress</span><span class="p">):</span></span>
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712
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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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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713
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">progress</span></span>
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<pre style="margin: 0;"> <span id="LC714" 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">@@ -746,14 +764,14 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_need_work_queue</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Queue</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># type: Queue</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_buffer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buffer_size</span></span>
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_assign_input</span><span class="p">(</span><span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path1</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">.</span><span class="n" style="color: #333;">interleaved</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC749" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_<span class="idiff left">assign_output</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">outfiles</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_<span class="idiff left">outfiles</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">outfiles</span></span></span>
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC769" 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>
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<pre style="margin: 0;"> <span id="LC770" 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="LC771" class="line" lang="python"> <span class="n" style="color: #333;">path1</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="LC772" class="line" lang="python"> <span class="n" style="color: #333;">path2</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="nb" style="color: #0086b3;">str</span><span class="p">]</span> <span class="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="LC773" class="line" lang="python"> <span class="n" style="color: #333;">interleaved</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">bool</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python"> <span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_two_input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_interleaved_input</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">interleaved</span></span>
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the workers read from these connections</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">@@ -770,9 +788,6 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span><span class="p">.</span><span class="n" style="color: #333;">daemon</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_reader_process</span><span class="p">.</span><span class="n" style="color: #333;">start</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC790" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_assign_output</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">:</span> <span class="n" style="color: #333;">OutputFiles</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC774" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_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="LC775" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_start_workers</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;">Tuple</span><span class="p">[</span><span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">WorkerProcess</span><span class="p">],</span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">Connection</span><span class="p">]]:</span></span>
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792
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="n" style="color: #333;">workers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC793" 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>
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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">@@ -789,16 +804,17 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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804
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<pre style="margin: 0;"> <span id="LC804" class="line" lang="python"> <span class="n" style="color: #333;">workers</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">worker</span><span class="p">)</span></span>
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790
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805
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<pre style="margin: 0;"> <span id="LC805" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">workers</span><span class="p">,</span> <span class="n" style="color: #333;">connections</span></span>
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806
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<pre style="margin: 0;"> <span id="LC806" class="line" lang="python"></span>
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792
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<pre style="margin: 0;">-<span id="LC792" 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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807
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<pre style="margin: 0;">+<span id="LC807" 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 class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Statistics</span></span><span class="p">:</span></span>
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808
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<pre style="margin: 0;"> <span id="LC808" 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="p">.</span><span class="n" style="color: #333;">_start_workers</span><span class="p">()</span></span>
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794
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809
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<pre style="margin: 0;"> <span id="LC809" 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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795
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">:</span></span>
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796
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811
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<pre style="margin: 0;"> <span id="LC811" class="line" lang="python"> <span class="n" style="color: #333;">writers</span><span class="p">.</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;">f</span><span class="p">))</span></span>
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797
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<pre style="margin: 0;">-<span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">stats</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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812
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<pre style="margin: 0;">+<span id="LC812" 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;"><span class="idiff left">Statistics</span></span><span class="p"><span class="idiff right">()</span></span></span>
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798
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813
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># A running total of the number of processed reads (for progress indicator)</span></span>
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799
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814
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">connections</span><span class="p">:</span></span>
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800
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815
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<pre style="margin: 0;"> <span id="LC815" class="line" lang="python"> <span class="n" style="color: #333;">ready_connections</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multiprocessing</span><span class="p">.</span><span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">wait</span><span class="p">(</span><span class="n" style="color: #333;">connections</span><span class="p">)</span></span>
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801
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816
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">connection</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ready_connections</span><span class="p">:</span></span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">,</span> <span class="n" style="color: #333;">Connection</span><span class="p">)</span></span>
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802
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818
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="python"> <span class="n" style="color: #333;">chunk_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>
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803
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819
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<pre style="margin: 0;"> <span id="LC819" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chunk_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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804
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820
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<pre style="margin: 0;"> <span id="LC820" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the worker is done</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -810,10 +826,7 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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810
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826
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<pre style="margin: 0;"> <span id="LC826" class="line" lang="python"> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">tb_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">connection</span><span class="p">.</span><span class="n" style="color: #333;">recv</span><span class="p">()</span></span>
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811
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827
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<pre style="margin: 0;"> <span id="LC827" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</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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812
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828
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<pre style="margin: 0;"> <span id="LC828" 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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813
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<pre style="margin: 0;">-<span id="LC813" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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814
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<pre style="margin: 0;">-<span id="LC814" 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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815
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<pre style="margin: 0;">-<span id="LC815" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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816
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<pre style="margin: 0;">-<span id="LC816" 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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829
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<pre style="margin: 0;">+<span id="LC829" 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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817
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830
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<pre style="margin: 0;"> <span id="LC830" class="line" lang="python"> <span class="n" style="color: #333;">connections</span><span class="p">.</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">connection</span><span class="p">)</span></span>
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818
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831
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<pre style="margin: 0;"> <span id="LC831" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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819
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">chunk_index</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); 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="857" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -844,11 +857,8 @@ class ParallelPipelineRunner(PipelineRunner):</td>
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844
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857
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<pre style="margin: 0;"> <span id="LC857" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_progress</span><span class="p">.</span><span class="n" style="color: #333;">stop</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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845
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">stats</span></span>
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846
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"></span>
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847
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<pre style="margin: 0;">-<span id="LC847" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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848
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<pre style="margin: 0;">-<span id="LC848" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">:</span></span>
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849
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<pre style="margin: 0;">-<span id="LC849" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO do not use hasattr</span></span>
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850
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<pre style="margin: 0;">-<span id="LC850" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdin</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">buffer</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="s" style="color: #d14;">'close'</span><span class="p">):</span></span>
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851
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<pre style="margin: 0;">-<span id="LC851" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC860" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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861
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<pre style="margin: 0;">+<span id="LC861" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_outfiles</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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852
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="python"></span>
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863
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"></span>
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SerialPipelineRunner</span><span class="p">(</span><span class="n" style="color: #333;">PipelineRunner</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">@@ -866,12 +876,14 @@ class SerialPipelineRunner(PipelineRunner):</td>
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876
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<pre style="margin: 0;"> <span id="LC876" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">().</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 class="n" style="color: #333;">progress</span><span class="p">)</span></span>
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867
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877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="python"> <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;">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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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="python"></span>
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869
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<pre style="margin: 0;">-<span id="LC869" 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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879
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<pre style="margin: 0;">+<span id="LC879" 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 class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Statistics</span></span><span class="p">:</span></span>
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880
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<pre style="margin: 0;"> <span id="LC880" 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="p">.</span><span class="n" style="color: #333;">_pipeline</span><span class="p">.</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="p">.</span><span class="n" style="color: #333;">_progress</span><span class="p">)</span></span>
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871
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_progress</span><span class="p">:</span></span>
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882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_progress</span><span class="p">.</span><span class="n" style="color: #333;">stop</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="LC883" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO</span></span>
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<pre style="margin: 0;">-<span id="LC874" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Statistics</span><span class="p">().</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;">total1_bp</span><span class="p">,</span> <span class="n" style="color: #333;">total2_bp</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;">_modifiers</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;">_filters</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC884" class="line" lang="python"> <span class="n" style="color: #333;">modifiers</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="p">.</span><span class="n" style="color: #333;">_pipeline</span><span class="p">,</span> <span class="s" style="color: #d14;">"_modifiers"</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="LC885" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">modifiers</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="LC886" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">Statistics</span><span class="p">().</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;">total1_bp</span><span class="p">,</span> <span class="n" style="color: #333;">total2_bp</span><span class="p">,</span> <span class="n" style="color: #333;">modifiers</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;">_filters</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC876" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC888" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff right">None</span></span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC889" class="line" lang="python"> <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;">close</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de"><strong>src/cutadapt/report.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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">Routines for printing a report.</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="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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4
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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;">from</span> <span class="nn" style="color: #555;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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5
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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;">import</span> <span class="nn" style="color: #555;">textwrap</span></span>
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6
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7
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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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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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">@@ -11,7 +12,8 @@ from .adapters import (</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="p">)</span></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;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">SingleEndModifier</span><span class="p">,</span> <span class="n" style="color: #333;">PairedModifier</span><span class="p">,</span> <span class="n" style="color: #333;">QualityTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">NextseqQualityTrimmer</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedAdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">ReverseComplementer</span><span class="p">)</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;">.filters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">WithStatistics</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>
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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;">.filters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">WithStatistics</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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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">CasavaFilter</span><span class="p">,</span> <span class="n" style="color: #333;">MaximumExpectedErrorsFilter</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">safe_divide</span><span class="p">(</span><span class="n" style="color: #333;">numerator</span><span class="p">,</span> <span class="n" style="color: #333;">denominator</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">@@ -38,6 +40,8 @@ class Statistics:</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</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>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</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="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</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="LC44" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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41
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45
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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 class="n" style="color: #333;">reverse_complemented</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span> <span class="c1" style="color: #998; font-style: italic;"># type: Optional[int]</span></span>
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42
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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43
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); 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="70" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -66,6 +70,9 @@ class Statistics:</td>
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66
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_short</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_if_not_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_short</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">too_short</span><span class="p">)</span></span>
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67
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_if_not_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_long</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">too_long</span><span class="p">)</span></span>
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68
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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_if_not_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_if_not_none</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">add_if_not_none</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span><span class="p">)</span></span>
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69
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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;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>
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70
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">total_bp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">total_bp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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71
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">other</span><span class="p">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -120,6 +127,10 @@ class Statistics:</td>
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120
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127
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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="p">.</span><span class="n" style="color: #333;">too_long</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">filtered</span></span>
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121
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128
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<pre style="margin: 0;"> <span id="LC128" 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;">w</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">):</span></span>
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122
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">filtered</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;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">MaximumExpectedErrorsFilter</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">filtered</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;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">CasavaFilter</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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">filtered</span></span>
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123
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python"></span>
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124
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_collect_modifier</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">:</span> <span class="n" style="color: #333;">SingleEndModifier</span><span class="p">):</span></span>
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125
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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;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">,</span> <span class="n" style="color: #333;">PairedAdapterCutter</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,6 +198,14 @@ class Statistics:</td>
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187
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">too_many_n_fraction</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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188
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">safe_divide</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_n</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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189
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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="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">too_many_expected_errors_fraction</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">safe_divide</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">casava_filtered_fraction</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">return</span> <span class="n" style="color: #333;">safe_divide</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"></span>
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190
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"></span>
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191
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">adapter_statistics</span><span class="p">:</span> <span class="n" style="color: #333;">EndStatistics</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_statistics</span><span class="p">.</span><span class="n" style="color: #333;">effective_length</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,8 +310,12 @@ def full_report(stats: Statistics, time: float, gc_content: float) -> str: # no</td>
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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">'file'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sio</span></span>
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292
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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293
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">print_s</span><span class="p">(</span><span class="s" style="color: #d14;">"Finished in {:.2F} s ({:.0F} µs/read; {:.2F} M reads/minute)."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="n" style="color: #333;">time</span><span class="p">,</span> <span class="mf" style="color: #099;">1E6</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">60</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1E6</span><span class="p">))</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;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">[:</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">6</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="n" style="color: #333;">micro</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"u"</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="python"> <span class="n" style="color: #333;">micro</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"µ"</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="n" style="color: #333;">print_s</span><span class="p">(</span><span class="s" style="color: #d14;">"Finished in {:.2F} s ({:.0F} {}s/read; {:.2F} M reads/minute)."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="n" style="color: #333;">time</span><span class="p">,</span> <span class="mf" style="color: #099;">1E6</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">micro</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">time</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">60</span> <span class="o" style="font-weight: 600;">/</span> <span class="mf" style="color: #099;">1E6</span><span class="p">))</span></span>
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296
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"></span>
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297
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">=== Summary ===</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">"</span></span>
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298
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321
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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;">stats</span><span class="p">.</span><span class="n" style="color: #333;">paired</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); 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="332" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -309,12 +332,19 @@ def full_report(stats: Statistics, time: float, gc_content: float) -> str: # no</td>
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309
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332
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">reverse_complemented</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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310
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333
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"Reverse-complemented: "</span> \</span>
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311
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334
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="s" style="color: #d14;">"{o.reverse_complemented:13,d} ({o.reverse_complemented_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></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;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_short</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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313
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<td class="diff-line-num new_line" data-linenumber="337" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
337
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{pairs_or_reads} that were too short: {o.too_short:13,d} ({o.too_short_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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314
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338
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_long</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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315
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<td class="diff-line-num new_line" data-linenumber="339" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
339
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{pairs_or_reads} that were too long: {o.too_long:13,d} ({o.too_long_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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316
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<td class="diff-line-num new_line" data-linenumber="340" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
340
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_many_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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<td class="diff-line-num old_line" data-linenumber="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
317
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<td class="diff-line-num new_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
341
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{pairs_or_reads} with too many N: {o.too_many_n:13,d} ({o.too_many_n_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); 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="342" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); 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="343" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{pairs_or_reads} with too many exp. errors: "</span> \</span>
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<td class="diff-line-num new old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); 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="344" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="python"> <span class="s" style="color: #d14;">"{o.too_many_expected_errors:13,d} ({o.too_many_expected_errors_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="345" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="346" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"{pairs_or_reads} failed CASAVA filter: "</span> \</span>
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<td class="diff-line-num new new_line" data-linenumber="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="s" style="color: #d14;">"{o.casava_filtered:13,d} ({o.casava_filtered_fraction:.1%})</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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318
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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319
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="n" style="color: #333;">report</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">textwrap</span><span class="p">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""</span><span class="se" style="color: #d14;">\</span></span>
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320
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"><span class="s" style="color: #d14;"> {pairs_or_reads} written (passing filters): {o.written:13,d} ({o.written_fraction:.1%})</span></span>
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<li id="af95dfcb30a51908f338d0fd6a196b9e4c108046">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#af95dfcb30a51908f338d0fd6a196b9e4c108046"><strong>src/cutadapt/utils.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,6 +194,7 @@ class FileOpener:</td>
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194
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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195
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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196
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<td class="diff-line-num new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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;">e</span><span class="p">.</span><span class="n" style="color: #333;">errno</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">errno</span><span class="p">.</span><span class="n" style="color: #333;">EMFILE</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;"># Too many open files</span></span>
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<td class="diff-line-num new old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"Too many open files, attempting to raise soft limit"</span><span class="p">)</span></span>
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197
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="n" style="color: #333;">raise_open_files_limit</span><span class="p">(</span><span class="mi" style="color: #099;">8</span><span class="p">)</span></span>
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198
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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;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">dnaio_open</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>
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199
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#8c2d0080c52c32f46cd635f520892470a0d177ef"><strong>tests/cut/action_retain.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>r1</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGTCCGAAcaag</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>r2</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">caag</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>r3</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">TGCCCTAGTcaag</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>r4</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">TGCCCTAGTcaa</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">>r5</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ggttaaCCGCCTTGA</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>r6</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ggttaaCATTGCCCTAGTTTATT</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">>r7</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">ttaaGTTCATGT</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>r8</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">ACGTACGT</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#2c7b65f451d23b9c52d2a2bca5f1d6388e692dd8"><strong>tests/data/action_retain.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>r1</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">CGTCCGAAcaagCCTGCCACAT</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">>r2</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">caagACAAGACCT</span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">>r3</span>
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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="plaintext">TGCCCTAGTcaag</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">>r4</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">TGCCCTAGTcaa</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">>r5</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">TGTTGggttaaCCGCCTTGA</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">>r6</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">ggttaaCATTGCCCTAGTTTATT</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">>r7</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">ttaaGTTCATGT</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">>r8</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">ACGTACGT</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#8b386ef32463372ea7de22d96d0771a85c1ed553"><strong>tests/test_command.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="s" style="color: #d14;">"""Tests that run the program in a subprocess"""</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</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;">sys</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></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;">utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">datapath</span><span class="p">,</span> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">,</span> <span class="n" style="color: #333;">cutpath</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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9
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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_run_cutadapt_process</span><span class="p">():</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">([</span><span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">])</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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12
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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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_run_as_module</span><span class="p">():</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check that "python3 -m cutadapt ..." works"""</span></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;">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="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">py</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;">assert</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">decode</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_standard_input_pipe</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""Read FASTQ from standard input"""</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">in_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use 'cat' to simulate that no file name is available for stdin</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="s" style="color: #d14;">"cat"</span><span class="p">,</span> <span class="n" style="color: #333;">in_path</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cat</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC28" 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 class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cat</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">py</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;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">cat</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">close</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;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC34" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_standard_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTQ to standard output (not using --output/-o option)"""</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC40" 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;">out_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;">out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC43" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_explicit_standard_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTQ to standard output (using "-o -")"""</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="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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;">out_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;">out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC56" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC59" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="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="LC62" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_force_fasta_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTA to standard output even on FASTQ input"""</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fasta"</span><span class="p">))</span></span>
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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;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="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;">out_file</span><span class="p">:</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;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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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;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC69" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fasta"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_non_utf8_locale</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="p">[</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"/dev/null"</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>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">env</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">"LC_CTYPE"</span><span class="p">:</span> <span class="s" style="color: #d14;">"C"</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#83ff0d8e113228f36b352922cbbb938d0aa9384b"><strong>tests/test_commandline.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;">os</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="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</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="LC4" 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;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span><span class="p">,</span> <span class="n" style="color: #333;">BytesIO</span></span>
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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;">pytest</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;">subprocess</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 class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.__main__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span></span>
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<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;">utils</span> <span class="kn" style="font-weight: 600;">import</span> <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="n" style="color: #333;">cutpath</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">@@ -54,7 +51,7 @@ def test_debug():</td>
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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>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_debug_trace</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--debug<span class="idiff left right">=trace</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</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>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--debug<span class="idiff left">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"--debug</span>"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</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>
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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>
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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;">test_example</span><span class="p">(</span><span class="n" style="color: #333;">run</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">@@ -230,6 +227,15 @@ def test_action_lowercase(run):</td>
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227
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-b CAAG -n 3 --action=lowercase"</span><span class="p">,</span> <span class="s" style="color: #d14;">"action_lowercase.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"action_lowercase.fasta"</span><span class="p">)</span></span>
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231
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228
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_action_retain</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-g GGTTAACC -a CAAG --action=retain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"action_retain.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"action_retain.fasta"</span><span class="p">)</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"></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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<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_action_retain_times</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="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ACGT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--times=2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--action=retain"</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>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_gz_multiblock</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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234
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python"> <span class="s" style="color: #d14;">"""compressed gz file with multiple blocks (created by concatenating two .gz files)"""</span></span>
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-b TTAGACATATCTCCGTCG"</span><span class="p">,</span> <span class="s" style="color: #d14;">"small.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"multiblock.fastq.gz"</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">@@ -470,9 +476,9 @@ def test_adapter_file_empty_name(run):</td>
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470
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476
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-N -a file:'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'adapter-empty-name.fasta'</span><span class="p">),</span> <span class="s" style="color: #d14;">'illumina.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'illumina.fastq.gz'</span><span class="p">)</span></span>
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471
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477
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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python"></span>
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478
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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC473" class="line" lang="python"><span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">test_demultiplex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">-<span id="LC474" class="line" lang="python"><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">tempdir</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tempfile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mkdtemp</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">prefix</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'cutadapt-tests.'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="python"> <span class="n" style="color: #333;">multiout</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">os</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">path</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">join</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tempdir</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'tmp-demulti.{name}.fasta'</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"><span class="o" style="font-weight: 600;"><span class="idiff left">@</span></span><span class="n" style="color: #333;"><span class="idiff">pytest</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">mark</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">parametrize</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"ext"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">".gz"</span></span><span class="p"><span class="idiff right">])</span></span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="python"><span class="k" style="font-weight: 600;"><span class="idiff left">def</span></span><span class="idiff"> </span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">test_demultiplex</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">cores</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">tmp_path</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ext</span></span><span class="p"><span class="idiff right">):</span></span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="python"> <span class="n" style="color: #333;">multiout</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">tmp_path</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'tmp-demulti.{name}.fasta'</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ext</span></span></span>
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<pre style="margin: 0;"> <span id="LC482" 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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483
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<pre style="margin: 0;"> <span id="LC483" 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="LC484" class="line" lang="python"> <span class="s" style="color: #d14;">'-a'</span><span class="p">,</span> <span class="s" style="color: #d14;">'first=AATTTCAGGAATT'</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">@@ -481,10 +487,13 @@ def test_demultiplex(cores):</td>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'twoadapters.fasta'</span><span class="p">),</span></span>
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488
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python"> <span class="p">]</span></span>
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489
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"> <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>
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<pre style="margin: 0;">-<span id="LC484" 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;">'twoadapters.first.fasta'</span><span class="p">),</span> <span class="n" style="color: #333;">multiout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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;">'first'</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;">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;">'twoadapters.second.fasta'</span><span class="p">),</span> <span class="n" style="color: #333;">multiout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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;">'second'</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;">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;">'twoadapters.unknown.fasta'</span><span class="p">),</span> <span class="n" style="color: #333;">multiout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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;">'unknown'</span><span class="p">))</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="python"> <span class="n" style="color: #333;">shutil</span><span class="p">.</span><span class="n" style="color: #333;">rmtree</span><span class="p">(</span><span class="n" style="color: #333;">tempdir</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"first"</span><span class="p">,</span> <span class="s" style="color: #d14;">"second"</span><span class="p">,</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">):</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">multiout</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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="LC492" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">".gz"</span><span class="p">:</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"gzip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="p">],</span> <span class="n" style="color: #333;">check</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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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">actual</span><span class="p">[:</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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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"twoadapters.{name}.fasta"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</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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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">expected</span><span class="p">,</span> <span class="n" style="color: #333;">actual</span><span class="p">)</span></span>
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497
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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python"></span>
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498
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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_multiple_fake_anchored_adapters</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -610,10 +619,6 @@ def test_negative_length(run):</td>
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'--length -5'</span><span class="p">,</span> <span class="s" style="color: #d14;">'shortened-negative.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)</span></span>
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_run_cutadapt_process</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC614" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">([</span><span class="s" style="color: #d14;">'cutadapt'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--version'</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC615" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC616" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">timeout</span><span class="p">(</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_296</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Hang when using both --no-trim and --info-file together</span></span>
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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">@@ -636,7 +641,8 @@ def test_adapterx(run):</td>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_discard_casava</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC639" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'--discard-casava'</span><span class="p">,</span> <span class="s" style="color: #d14;">'casava.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'casava.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="python"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'--discard-casava'</span><span class="p">,</span> <span class="s" style="color: #d14;">'casava.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'casava.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">casava_filtered</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_underscore</span><span class="p">(</span><span class="n" style="color: #333;">run</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">@@ -663,68 +669,6 @@ def test_paired_separate(run):</td>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-a CAGTGGAGTA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"paired-separate.2.fastq"</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="LC670" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC671" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_run_as_module</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check that "python3 -m cutadapt ..." works"""</span></span>
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<pre style="margin: 0;">-<span id="LC668" 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="LC669" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--version"</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">].</span><span class="n" style="color: #333;">decode</span><span class="p">().</span><span class="n" style="color: #333;">strip</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;">-<span id="LC671" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC672" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_standard_input_pipe</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC674" class="line" lang="python"> <span class="s" style="color: #d14;">"""Read FASTQ from standard input"""</span></span>
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<pre style="margin: 0;">-<span id="LC675" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">in_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Use 'cat' to simulate that no file name is available for stdin</span></span>
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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span><span class="s" style="color: #d14;">"cat"</span><span class="p">,</span> <span class="n" style="color: #333;">in_path</span><span class="p">],</span> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">PIPE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cat</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC681" 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 class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;">out_path</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">stdin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cat</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="python"> <span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">py</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python"> <span class="n" style="color: #333;">cat</span><span class="p">.</span><span class="n" style="color: #333;">stdout</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC686" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC687" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC688" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC689" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_standard_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC691" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTQ to standard output (not using --output/-o option)"""</span></span>
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<pre style="margin: 0;">-<span id="LC692" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC693" 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;">out_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;">out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC694" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC695" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC696" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC697" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC699" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC700" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC701" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC702" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_explicit_standard_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC703" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTQ to standard output (using "-o -")"""</span></span>
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<pre style="margin: 0;">-<span id="LC704" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC705" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC706" 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;">out_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;">out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC707" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC709" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC710" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC712" 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.fastq"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_force_fasta_output</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC716" class="line" lang="python"> <span class="s" style="color: #d14;">"""Write FASTA to standard output even on FASTQ input"""</span></span>
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<pre style="margin: 0;">-<span id="LC717" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC718" class="line" lang="python"> <span class="n" style="color: #333;">out_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fasta"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC719" 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;">out_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;">out_file</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">py</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">Popen</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC721" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cutadapt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC722" 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 class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fastq"</span><span class="p">)],</span></span>
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<pre style="margin: 0;">-<span id="LC723" class="line" lang="python"> <span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">out_file</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC724" class="line" lang="python"> <span class="n" style="color: #333;">_</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">py</span><span class="p">.</span><span class="n" style="color: #333;">communicate</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC725" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="s" style="color: #d14;">"small.fasta"</span><span class="p">),</span> <span class="n" style="color: #333;">out_path</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC726" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC727" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC672" 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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<pre style="margin: 0;"> <span id="LC673" 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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<pre style="margin: 0;"> <span id="LC674" 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">@@ -773,7 +717,8 @@ def test_reverse_complement_and_info_file(run, tmp_path, cores):</td>
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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_max_expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--max-ee=0.9"</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxee.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxee.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--max-ee=0.9"</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxee.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"maxee.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">too_many_expected_errors</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="LC722" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC724" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_max_expected_errors_fasta</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">):</span></span>
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<li id="aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#aa2f4f1f576921437d23bf4a4f1dd29ac1cbacda"><strong>tests/test_modifiers.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;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">List</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;">import</span> <span class="nn" style="color: #555;">pytest</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;">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="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;">BackAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedPrefixAdapters</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;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BackAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">IndexedPrefixAdapters</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="LC7" class="line" lang="python"> <span class="n" style="color: #333;">FrontAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">Adapter</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;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</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;">QualityTrimmer</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"> <span class="n" style="color: #333;">Shortener</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedAdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">,</span> <span class="n" style="color: #333;">ZeroCapper</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +83,8 @@ def test_adapter_cutter_indexing():</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCGGTTAACCCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTTAACCGGTTTT"</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="p">(</span><span class="s" style="color: #d14;">"trim"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTT"</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="p">(</span><span class="s" style="color: #d14;">"lowercase"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCggttaacccc"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTTaaccggtttt"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"mask"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCNNNNNNNNNN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTTNNNNNNNNNN"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"mask"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCNNNNNNNNNN"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTTNNNNNNNNNN"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"retain"</span><span class="p">,</span> <span class="s" style="color: #d14;">"CCCCGGTTAA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTTTAACCGG"</span><span class="p">),</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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_paired_adapter_cutter_actions</span><span class="p">(</span><span class="n" style="color: #333;">action</span><span class="p">,</span> <span class="n" style="color: #333;">expected_trimmed1</span><span class="p">,</span> <span class="n" style="color: #333;">expected_trimmed2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">a1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BackAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">"GGTTAA"</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">@@ -93,3 +97,37 @@ def test_paired_adapter_cutter_actions(action, expected_trimmed1, expected_trimm</td>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">trimmed1</span><span class="p">,</span> <span class="n" style="color: #333;">trimmed2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pac</span><span class="p">(</span><span class="n" style="color: #333;">s1</span><span class="p">,</span> <span class="n" style="color: #333;">s2</span><span class="p">,</span> <span class="n" style="color: #333;">info1</span><span class="p">,</span> <span class="n" style="color: #333;">info2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expected_trimmed1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">trimmed1</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span></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;">assert</span> <span class="n" style="color: #333;">expected_trimmed2</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">trimmed2</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_retain_times</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">BackAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">"ACGT"</span><span class="p">)],</span> <span class="n" style="color: #333;">times</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"retain"</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;">assert</span> <span class="s" style="color: #d14;">"cannot be combined with times"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">value</span><span class="p">.</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"></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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_action_retain</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="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BackAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">"AACCGG"</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;">ac</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;">back</span><span class="p">],</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"retain"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r1"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ATTGCCAACCGGTATATAT"</span><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="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ac</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"ATTGCCAACCGG"</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">trimmed</span><span class="p">.</span><span class="n" style="color: #333;">sequence</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>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="p">.</span><span class="n" style="color: #333;">mark</span><span class="p">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"s,expected"</span><span class="p">,</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ATTATTggttaaccAAAAAaaccggTATT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ggttaaccAAAAAaaccgg"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"AAAAAaaccggTATT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"AAAAAaaccgg"</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"ATTATTggttaaccAAAAA"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ggttaaccAAAAA"</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;">"ATTATT"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ATTATT"</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>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_action_retain</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python"> <span class="n" style="color: #333;">front</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FrontAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">"GGTTAACC"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BackAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">"AACCGG"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span><span class="p">:</span> <span class="n" style="color: #333;">List</span><span class="p">[</span><span class="n" style="color: #333;">Adapter</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="LC127" class="line" lang="python"> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">(</span><span class="n" style="color: #333;">front</span><span class="p">,</span> <span class="n" style="color: #333;">back</span><span class="p">,</span> <span class="n" style="color: #333;">front_required</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;">back_required</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;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"linked"</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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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">ac</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;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"retain"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">"r1"</span><span class="p">,</span> <span class="n" style="color: #333;">s</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;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">(</span><span class="n" style="color: #333;">seq</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;">trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ac</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">,</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">trimmed</span><span class="p">.</span><span class="n" style="color: #333;">sequence</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/02bef8f81a3ff83013340ae5ab51880b970c2bbf#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c"><strong>tox.ini</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">@@ -13,6 +13,7 @@ commands =</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">coverage</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">run</span> <span class="py">--concurrency</span><span class="p">=</span><span class="s" style="color: #d14;">multiprocessing -m pytest --doctest-modules --pyargs cutadapt tests</span></span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">coverage</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">combine</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">coverage</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">report</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">coverage</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">xml</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="ini"><span class="nn" style="color: #555;">[testenv:docs]</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="ini"><span class="py">basepython</span> <span class="p">=</span> <span class="s" style="color: #d14;">python3.6</span></span>
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