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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-cutadapt">Debian Med / python-cutadapt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30">afc23835</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-03-31T16:14:54+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.9</pre>
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<h4>28 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#4990be809a537bf86e4be2fe2e8251c83d8bd129">
CHANGES.rst
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<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<li class="file-stats">
<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">
doc/conf.py
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<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">
doc/guide.rst
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<li class="file-stats">
<a href="#6677207c6fa30ac9cec19ad036ae842582159ecb">
doc/installation.rst
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<a href="#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
pyproject.toml
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<li class="file-stats">
<a href="#babdfe5d368a4907abadce7f9b00dfab2489185a">
src/cutadapt/__main__.py
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<a href="#8fb347891ec0a40b16ef2bdbe361f823e12aa016">
src/cutadapt/adapters.py
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<a href="#6ed465db6839a69141086c2acf1dc01a8b17a981">
src/cutadapt/filters.py
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<a href="#a44086ebe255bc0df91ea1d82811c828e6f5e324">
src/cutadapt/modifiers.py
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<li class="file-stats">
<a href="#1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">
src/cutadapt/pipeline.py
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<a href="#5a4a773b73e0bdb43c051d1b039d337cd428e3e1">
src/cutadapt/qualtrim.pyx
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<a href="#0947279ab1fb32f21dde9a563c2b4ca1cd2fc0de">
src/cutadapt/report.py
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tests/cut/maxee.fastq
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−
tests/data/SRR2040271_1.fastq
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tests/data/maxee.fastq
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tests/data/plus.fastq
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<a href="#4c91f80a781e5621e92c74fdd1bddaa8ef6b43e7">
tests/test_adapters.py
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<li class="file-stats">
<a href="#83ff0d8e113228f36b352922cbbb938d0aa9384b">
tests/test_commandline.py
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<a href="#124a8b77d32c7ca9f7f1966a0cde3894ce860e05">
tests/test_main.py
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<a href="#4ad7124461a591ee5c5c2e30f24380a477c3ed52">
tests/test_paired.py
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<a href="#9627b71ff9952493fda5865aea912319edd1cdd2">
tests/test_parser.py
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<a href="#a29298d28cfcb546445a18cc3462646626165ac4">
tests/test_qualtrim.py
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<a href="#bb92bf4985f91906d71414ff1f007cc598adff83">
tests/test_trim.py
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<a href="#570726290219a04b926b9aa2c02fe1ba4204124a">
tests/utils.py
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<li class="file-stats">
<a href="#61be067c7cf3bdbf8a6b021a2b5167eb30612d0c">
tox.ini
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,3 +15,4 @@ __pycache__/</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">/doc/_build</span>
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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="plaintext">/src/cutadapt.egg-info/</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">src/cutadapt/_version.py</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="plaintext">.mpypy_cache</span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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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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<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">
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></span>
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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">cache</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"></span>
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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>
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<td class="diff-line-num new_line old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">nightly"</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"></span>
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16
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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;">install</span><span class="pi">:</span></span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install <span class="idiff left right">'Cython>=0.28' tox-travis</span></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 <span class="idiff left right">tox</span></span></span>
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18
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"></span>
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19
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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;">script</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="pi">-</span> <span class="s" style="color: #d14;">tox</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">@@ -31,6 +22,30 @@ env:</td>
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31
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"></span>
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23
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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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<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;">3.5"</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;">env</span><span class="pi">:</span> <span class="s" style="color: #d14;">TOXENV=py35</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;">3.6"</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=py36</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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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;">3.7"</span></span>
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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=py37</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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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;">3.8"</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=py38</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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<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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<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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<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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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"></span>
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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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<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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<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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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"></span>
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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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<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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -44,10 +59,5 @@ jobs:</td>
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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="LC47" 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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<pre style="margin: 0;">-<span id="LC48" 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="LC49" 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 flake8</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">flake8 src/ tests/</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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/afc23835c3b1b22776876ed5f9011295b0059b30#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 +2,17 @@</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;">v2</span><span class="m" style="color: #099;">.9</span> <span class="p">(</span><span class="m" style="color: #099;">2020</span><span class="p">-</span><span class="m" style="color: #099;">03</span><span class="p">-</span><span class="m" style="color: #099;">18</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;">441</span><span class="p">`:</span> <span class="n" style="color: #333;">Add</span> <span class="n" style="color: #333;">a</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="p">(</span><span class="k" style="font-weight: 600;">or</span> <span class="p">``--</span><span class="k" style="font-weight: 600;">max</span><span class="p">-</span><span class="n" style="color: #333;">expected</span><span class="p">-</span><span class="n" style="color: #333;">errors</span><span class="p">``)</span> <span class="n" style="color: #333;">option</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">filtering</span> <span class="n" style="color: #333;">reads</span> <span class="n" style="color: #333;">whose</span> <span class="n" style="color: #333;">number</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">expected</span> <span class="n" style="color: #333;">errors</span> <span class="n" style="color: #333;">exceeds</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">given</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">threshold</span><span class="p">.</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">idea</span> <span class="n" style="color: #333;">comes</span> <span class="k" style="font-weight: 600;">from</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"> <span class="p">`</span><span class="n" style="color: #333;">Edgar</span> <span class="n" style="color: #333;">et</span> <span class="n" style="color: #333;">al</span><span class="p">.</span> <span class="p">(</span><span class="m" style="color: #099;">2015</span><span class="p">)</span> <span class="p"><</span><span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">academic</span><span class="p">.</span><span class="n" style="color: #333;">oup</span><span class="p">.</span><span class="n" style="color: #333;">com</span><span class="p">/</span><span class="n" style="color: #333;">bioinformatics</span><span class="p">/</span><span class="n" style="color: #333;">article</span><span class="p">/</span><span class="m" style="color: #099;">31</span><span class="p">/</span><span class="m" style="color: #099;">21</span><span class="p">/</span><span class="m" style="color: #099;">3476</span><span class="p">/</span><span class="m" style="color: #099;">194979</span><span class="p">>`</span><span class="n" style="color: #333;">_</span><span class="p">.</span></span>
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<td class="diff-line-num 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">
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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;">438</span><span class="p">`:</span> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">info</span> <span class="n" style="color: #333;">file</span> <span class="n" style="color: #333;">now</span> <span class="n" style="color: #333;">contains</span> <span class="n" style="color: #333;">the</span> <span class="p">``</span> <span class="n" style="color: #333;">rc</span><span class="p">``</span> <span class="n" style="color: #333;">suffix</span> <span class="n" style="color: #333;">that</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">added</span> <span class="k" style="font-weight: 600;">to</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">names</span> <span class="k" style="font-weight: 600;">of</span> <span class="nb" style="color: #0086b3;">reverse</span><span class="p">-</span><span class="n" style="color: #333;">complemented</span> <span class="n" style="color: #333;">reads</span> <span class="p">(</span><span class="k" style="font-weight: 600;">with</span> <span class="p">``--</span><span class="n" style="color: #333;">revcomp</span><span class="p">``).</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="p">*</span> <span class="p">:</span><span class="n" style="color: #333;">issue</span><span class="p">:`</span><span class="m" style="color: #099;">448</span><span class="p">`:</span> <span class="p">``.</span><span class="n" style="color: #333;">bz2</span><span class="p">``</span> <span class="k" style="font-weight: 600;">and</span> <span class="p">``.</span><span class="n" style="color: #333;">xz</span><span class="p">``</span> <span class="n" style="color: #333;">output</span> <span class="n" style="color: #333;">wasn</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">’</span><span class="n" style="color: #333;">t</span> <span class="n" style="color: #333;">possible</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">multi</span><span class="p">-</span><span class="n" style="color: #333;">core</span> <span class="n" style="color: #333;">mode</span><span class="p">.</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">v2</span><span class="m" style="color: #099;">.8</span> <span class="p">(</span><span class="m" style="color: #099;">2020</span><span class="p">-</span><span class="m" style="color: #099;">01</span><span class="p">-</span><span class="m" style="color: #099;">13</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>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Copyright (c) 2010-20<span class="idiff left right">19</span> Marcel Martin <marcel.martin@scilifelab.se></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Copyright (c) 2010-20<span class="idiff left right">20</span> Marcel Martin <marcel.martin@scilifelab.se></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Permission is hereby granted, free of charge, to any person obtaining a copy</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">of this software and associated documentation files (the "Software"), to deal</span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,6 +14,7 @@</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC16" 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="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If extensions (or modules to document with autodoc) are in another directory,</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add these directories to sys.path here. If the directory is relative to the</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,8 +47,8 @@ source_suffix = '.rst'</td>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">master_doc</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'index'</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">u</span>'Cutadapt'</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">u'2010-2019, Marcel Martin'</span></span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Cutadapt'</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left">'2010-{}, Marcel Martin'</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">time</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gmtime</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tm_year</span></span><span class="p"><span class="idiff right">)</span></span></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="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -807,10 +807,12 @@ Searching reverse complements</td>
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<pre style="margin: 0;"> <span id="LC807" class="line" lang="plaintext">-----------------------------</span>
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="plaintext">.. note::</span>
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<pre style="margin: 0;">-<span id="LC810" class="line" lang="plaintext"> Option ``--revcomp`` is added on a tentative basis. Its behaviour</span>
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="plaintext"> Option ``--revcomp`` is added on a tentative basis. Its behaviour may change in the next</span>
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="plaintext"> releases.</span>
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<pre style="margin: 0;"> <span id="LC812" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC813" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC814" class="line" lang="plaintext">By default, Cutadapt expects adapters to be given in the same orientation (5' to 3') as the reads.</span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="plaintext">That is, neither reads nor adapters are reverse-complemented.</span>
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<pre style="margin: 0;"> <span id="LC816" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC817" class="line" lang="plaintext">To change this, use option ``--revcomp`` or its abbreviation ``--rc``. If given, Cutadapt searches</span>
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<pre style="margin: 0;"> <span id="LC818" class="line" lang="plaintext">both the read and its reverse complement for adapters. If the reverse complemented read yields</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">@@ -1122,6 +1124,12 @@ reads. They always discard those reads for which the filtering criterion applies</td>
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<pre style="margin: 0;"> <span id="LC1124" class="line" lang="plaintext"> Discard reads with more than COUNT ``N`` bases. If ``COUNT_or_FRACTION`` is</span>
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<pre style="margin: 0;"> <span id="LC1125" class="line" lang="plaintext"> a number between 0 and 1, it is interpreted as a fraction of the read length</span>
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<pre style="margin: 0;"> <span id="LC1126" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC1127" class="line" lang="plaintext">``--max-expected-errors ERRORS`` or ``--max-ee ERRORS``</span>
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<pre style="margin: 0;">+<span id="LC1128" class="line" lang="plaintext"> Discard reads with more than ERRORS expected errors. The number of expected</span>
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<pre style="margin: 0;">+<span id="LC1129" class="line" lang="plaintext"> errors is computed as described in</span>
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<pre style="margin: 0;">+<span id="LC1130" class="line" lang="plaintext"> `Edgar et al. (2015) <https://academic.oup.com/bioinformatics/article/31/21/3476/194979>`_,</span>
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<pre style="margin: 0;">+<span id="LC1131" class="line" lang="plaintext"> (Section 2.2).</span>
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<pre style="margin: 0;">+<span id="LC1132" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC1133" class="line" lang="plaintext">``--discard-casava``</span>
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<pre style="margin: 0;"> <span id="LC1134" class="line" lang="plaintext"> Discard reads that did not pass CASAVA filtering. Illumina’s CASAVA pipeline in</span>
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<pre style="margin: 0;"> <span id="LC1135" class="line" lang="plaintext"> version 1.8 adds an *is_filtered* header field to each read. Specifying this</span>
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<li id="6677207c6fa30ac9cec19ad036ae842582159ecb">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#6677207c6fa30ac9cec19ad036ae842582159ecb"><strong>doc/installation.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,7 +11,7 @@ Quick installation</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">The easiest way to install Cutadapt is to use ``pip3`` on the command line::</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"> p<span class="idiff left right">ip3</span> install --user --upgrade cutadapt</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> p<span class="idiff left right">ython3 -m pip</span> install --user --upgrade cutadapt</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">This will download the software from `PyPI (the Python packaging</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">index) <https://pypi.python.org/pypi/cutadapt/>`_, and</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">@@ -28,14 +28,30 @@ If you want to avoid typing the full path, add the directory</td>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Installation with conda</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">-----------------------</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">Alternatively, Cutadapt is available as a conda package from the</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">`bioconda channel <https://bioconda.github.io/>`_. If you do not have conda,</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">`install miniconda <http://conda.pydata.org/miniconda.html>`_ first.</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">Then install Cutadapt like this::</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Alternatively, Cutadapt is available as a Conda package from the</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">`bioconda channel <https://bioconda.github.io/>`_.</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">`Install miniconda <http://conda.pydata.org/miniconda.html>`_ if</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">you don’t have Conda. Then follow the `Bioconda installation</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">instructions <https://bioconda.github.io/user/install.html>`_ (in particular,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">make sure you have both `bioconda` and `conda-forge` in your channels list).</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"><span class="idiff left right"> conda install -c bioconda cutadapt</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"><span class="idiff left right">To then install Cutadapt into a new Conda environment, use this command::</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">If neither ``pip`` nor ``conda`` installation works, keep reading.</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> conda create -n cutadaptenv cutadapt</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Here, ``cutadaptenv`` is the name of the Conda environment. (You can</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">choose a different name.)</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">An environment needs to be activated every time you want to use the</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">programs in it::</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> conda activate cutadaptenv</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Finally, check whether it worked::</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> cutadapt --version</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">This should show the Cutadapt version number.</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Installation on a Debian-based Linux distribution</span>
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<li id="5d07e7d72637aa0d59c89d381fe6dc4cf46e2491">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#5d07e7d72637aa0d59c89d381fe6dc4cf46e2491"><strong>pyproject.toml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="toml"><span class="nn" style="color: #555;">[build-system]</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="toml"><span class="py">requires</span> <span class="p">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"setuptools"</span><span class="p">,</span> <span class="s" style="color: #d14;">"wheel"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setuptools_scm"</span><span class="p">,</span> <span class="s" style="color: #d14;">"cython"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="toml"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="toml"><span class="nn" style="color: #555;">[black.tool]</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="toml"><span class="py">line-length</span> <span class="p">=</span> <span class="mi" style="color: #099;">100</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#babdfe5d368a4907abadce7f9b00dfab2489185a"><strong>src/cutadapt/__main__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2010-20<span class="idiff left right">19</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2010-20<span class="idiff left right">20</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Permission is hereby granted, free of charge, to any person obtaining a copy</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># of this software and associated documentation files (the "Software"), to deal</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">@@ -23,7 +23,7 @@</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;">cutadapt version {version}</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (C) 2010-20<span class="idiff left right">19</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;">Copyright (C) 2010-20<span class="idiff left right">20</span> Marcel Martin <marcel.martin@scilifelab.se></span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="s" style="color: #d14;">cutadapt removes adapter sequences from high-throughput sequencing reads.</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ import sys</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">time</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<pre style="margin: 0;">-<span id="LC60" 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;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span><span class="p">,</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">Union</span></span>
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<pre style="margin: 0;">+<span id="LC60" 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;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Sequence</span><span class="p">,</span> <span class="n" style="color: #333;">List</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span><span class="p">,</span> <span class="n" style="color: #333;">Iterator</span><span class="p">,</span> <span class="n" style="color: #333;">Union</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Type</span></span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">,</span> <span class="n" style="color: #333;">SUPPRESS</span><span class="p">,</span> <span class="n" style="color: #333;">HelpFormatter</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -65,13 +65,13 @@ import dnaio</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">warn_duplicate_adapters</span><span class="p">,</span> <span class="n" style="color: #333;">Adapter</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.parser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterParser</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Modifier</span><span class="p">,</span> <span class="n" style="color: #333;">LengthTagModifier</span><span class="p">,</span> <span class="n" style="color: #333;">SuffixRemover</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixSuffixAdder</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">,</span> <span class="n" style="color: #333;">LengthTagModifier</span><span class="p">,</span> <span class="n" style="color: #333;">SuffixRemover</span><span class="p">,</span> <span class="n" style="color: #333;">PrefixSuffixAdder</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">ZeroCapper</span><span class="p">,</span> <span class="n" style="color: #333;">QualityTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">UnconditionalCutter</span><span class="p">,</span> <span class="n" style="color: #333;">NEndTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">PairedAdapterCutterError</span><span class="p">,</span> <span class="n" style="color: #333;">PairedAdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">NextseqQualityTrimmer</span><span class="p">,</span> <span class="n" style="color: #333;">Shortener</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">ReverseComplementer</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">full_report</span><span class="p">,</span> <span class="n" style="color: #333;">minimal_report</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.pipeline</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">SingleEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndPipeline</span><span class="p">,</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">OutputFiles</span><span class="p">,</span> <span class="n" style="color: #333;">SerialPipelineRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">OutputFiles</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">PipelineRunner</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">SerialPipelineRunner</span><span class="p">,</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">,</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span> <span class="n" style="color: #333;">DummyProgress</span><span class="p">,</span> <span class="n" style="color: #333;">FileOpener</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.log</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup_logging</span><span class="p">,</span> <span class="n" style="color: #333;">REPORT</span></span>
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<pre style="margin: 0;"> <span id="LC77" 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">@@ -248,6 +248,10 @@ def get_argument_parser() -> ArgumentParser:</td>
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248
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--max-n"</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;">float</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;">None</span><span class="p">,</span> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"COUNT"</span><span class="p">,</span></span>
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249
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<td class="diff-line-num new_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
249
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<pre style="margin: 0;"> <span id="LC249" 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;">"Discard reads with more than COUNT 'N' bases. If COUNT is a number "</span></span>
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250
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="s" style="color: #d14;">"between 0 and 1, it is interpreted as a fraction of the read length."</span><span class="p">)</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--max-expected-errors"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--max-ee"</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;">float</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;">None</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"ERRORS"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
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<pre style="margin: 0;">+<span id="LC253" 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;">"Discard reads whose expected number of errors (computed "</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="s" style="color: #d14;">"from quality values) exceeds ERRORS."</span><span class="p">)</span></span>
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251
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255
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--discard-trimmed"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--discard"</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>
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252
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<td class="diff-line-num new_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
256
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<pre style="margin: 0;"> <span id="LC256" 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;">"Discard reads that contain an adapter. Use also -O to avoid "</span></span>
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253
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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="s" style="color: #d14;">"discarding too many randomly matching reads."</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); 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="676" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -672,6 +676,7 @@ def pipeline_from_parsed_args(args, paired, file_opener) -> Pipeline:</td>
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672
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676
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<pre style="margin: 0;"> <span id="LC676" class="line" lang="python"> <span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>
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673
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677
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<pre style="margin: 0;"> <span id="LC677" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">,</span> <span class="n" style="color: #333;">lengths</span><span class="p">)</span></span>
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674
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678
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_expected_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_expected_errors</span></span>
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675
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680
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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_casava</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_casava</span></span>
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676
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_trimmed</span></span>
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677
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682
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<pre style="margin: 0;"> <span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_untrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_untrimmed</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); 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="769" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -764,7 +769,7 @@ def add_adapter_cutter(</td>
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764
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769
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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)</span></span>
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python"></span>
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC767" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">modifiers_applying_to_both_ends_if_paired</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;">Modifier</span><span class="p">]:</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">modifiers_applying_to_both_ends_if_paired</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="n" style="color: #333;">Iterator</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">]:</span></span>
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768
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</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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769
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">Shortener</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;">length</span><span class="p">)</span></span>
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770
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775
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<pre style="margin: 0;"> <span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">trim_n</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); 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="841" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -836,6 +841,11 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>
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836
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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;">cores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">available_cpu_count</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cores</span></span>
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837
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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;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FileOpener</span><span class="p">(</span></span>
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838
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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;">compression_level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">compression_level</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isatty</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="python"> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Progress</span><span class="p">()</span></span>
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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;">else</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="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DummyProgress</span><span class="p">()</span></span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="python"></span>
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839
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849
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<pre style="margin: 0;"> <span id="LC849" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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840
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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;">is_interleaved_input</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">determine_interleaved</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">)</span></span>
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841
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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;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">input_paired_filename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">setup_input_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">inputs</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="853" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -843,40 +853,19 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>
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<pre style="margin: 0;"> <span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">check_arguments</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="python"> <span class="n" style="color: #333;">pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline_from_parsed_args</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="python"> <span class="n" style="color: #333;">outfiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">open_output_files</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">default_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">is_interleaved_output</span><span class="p">,</span> <span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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856
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<pre style="margin: 0;">+<span id="LC856" class="line" lang="python"> <span class="n" style="color: #333;">infiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_paired_filename</span><span class="p">,</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="python"> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_interleaved_input</span><span class="p">)</span></span>
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858
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<pre style="margin: 0;">+<span id="LC858" class="line" lang="python"> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">setup_runner</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">cores</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;">buffer_size</span><span class="p">)</span></span>
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">CommandLineError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>
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862
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="python"></span>
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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;">cores</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="LC851" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">can_output_to</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC852" class="line" lang="python"> <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span></span>
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<pre style="margin: 0;">-<span id="LC853" class="line" lang="python"> <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC854" 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="LC855" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Running in parallel is currently not supported "</span></span>
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<pre style="margin: 0;">-<span id="LC856" class="line" lang="python"> <span class="s" style="color: #d14;">"when using --format or when demultiplexing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">-<span id="LC857" class="line" lang="python"> <span class="s" style="color: #d14;">"Omit --cores/-j to continue."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC858" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>
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<pre style="margin: 0;">-<span id="LC859" 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="LC860" class="line" lang="python"> <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SerialPipelineRunner</span></span>
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<pre style="margin: 0;">-<span id="LC861" class="line" lang="python"> <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC862" class="line" lang="python"> <span class="n" style="color: #333;">infiles</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">InputFiles</span><span class="p">(</span><span class="n" style="color: #333;">input_filename</span><span class="p">,</span> <span class="n" style="color: #333;">file2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">input_paired_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">interleaved</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">is_interleaved_input</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC864" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isatty</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC865" class="line" lang="python"> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Progress</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC866" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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867
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<pre style="margin: 0;">-<span id="LC867" class="line" lang="python"> <span class="n" style="color: #333;">progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">DummyProgress</span><span class="p">()</span></span>
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868
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<pre style="margin: 0;">-<span id="LC868" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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869
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<pre style="margin: 0;">-<span id="LC869" class="line" lang="python"> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runner_class</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">runner_kwargs</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC870" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</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="LC871" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC872" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="c1" style="color: #998; font-style: italic;"># avoid IDE warnings below</span></span>
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<pre style="margin: 0;">-<span id="LC873" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC863" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Processing reads on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d core</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s mode ..."</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="python"> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="s" style="color: #d14;">'s'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="python"> <span class="p">{</span><span class="bp" style="color: #999;">False</span><span class="p">:</span> <span class="s" style="color: #d14;">'single-end'</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span> <span class="s" style="color: #d14;">'paired-end'</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;">paired</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC878" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">stats</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runner</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">run</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">runner</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">close</span></span><span class="p">()</span></span>
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867
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<pre style="margin: 0;">+<span id="LC867" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">with</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">runner</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">as</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">r</span></span><span class="p"><span class="idiff right">:</span></span></span>
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868
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<pre style="margin: 0;">+<span id="LC868" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">stats</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">r</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">run</span></span><span class="p">()</span></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;">except</span> <span class="nb" style="color: #0086b3;">KeyboardInterrupt</span><span class="p">:</span></span>
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881
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Interrupted"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="p">)</span></span>
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">130</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">@@ -897,5 +886,26 @@ def main(cmdlineargs=None, default_outfile=sys.stdout.buffer):</td>
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886
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<pre style="margin: 0;"> <span id="LC886" class="line" lang="python"> <span class="n" style="color: #333;">pstats</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;">profiler</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort_stats</span><span class="p">(</span><span class="s" style="color: #d14;">'time'</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_stats</span><span class="p">(</span><span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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887
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<pre style="margin: 0;"> <span id="LC887" class="line" lang="python"></span>
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888
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<pre style="margin: 0;"> <span id="LC888" class="line" lang="python"></span>
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889
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<pre style="margin: 0;">+<span id="LC889" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">setup_runner</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">:</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC890" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">cores</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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891
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<pre style="margin: 0;">+<span id="LC891" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">can_output_to</span><span class="p">(</span><span class="n" style="color: #333;">outfiles</span><span class="p">):</span></span>
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892
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<pre style="margin: 0;">+<span id="LC892" class="line" lang="python"> <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ParallelPipelineRunner</span> <span class="c1" style="color: #998; font-style: italic;"># type: Type[PipelineRunner]</span></span>
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<pre style="margin: 0;">+<span id="LC893" class="line" lang="python"> <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">n_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">buffer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">buffer_size</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC894" 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="LC895" 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;">"Running in parallel is currently not supported "</span></span>
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<pre style="margin: 0;">+<span id="LC896" class="line" lang="python"> <span class="s" style="color: #d14;">"when using --format or when demultiplexing.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"> <span class="s" style="color: #d14;">"Omit --cores/-j to continue."</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># return # avoid IDE warnings below</span></span>
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899
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<pre style="margin: 0;">+<span id="LC899" 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="LC900" class="line" lang="python"> <span class="n" style="color: #333;">runner_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SerialPipelineRunner</span></span>
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">runner_kwargs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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903
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<pre style="margin: 0;">+<span id="LC903" class="line" lang="python"> <span class="n" style="color: #333;">runner</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">runner_class</span><span class="p">(</span><span class="n" style="color: #333;">pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">infiles</span><span class="p">,</span> <span class="n" style="color: #333;">outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">progress</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">runner_kwargs</span><span class="p">)</span></span>
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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="n" style="color: #333;">dnaio</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">UnknownFileFormat</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">IOError</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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905
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<pre style="margin: 0;">+<span id="LC905" 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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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">runner</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" class="line" lang="python"></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="python"></span>
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900
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910
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<pre style="margin: 0;"> <span id="LC910" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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901
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911
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<pre style="margin: 0;"> <span id="LC911" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<li id="8fb347891ec0a40b16ef2bdbe361f823e12aa016">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#8fb347891ec0a40b16ef2bdbe361f823e12aa016"><strong>src/cutadapt/adapters.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -181,6 +181,7 @@ class AdapterStatistics:</td>
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181
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"></span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Match</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>
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184
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185
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<pre style="margin: 0;"> <span id="LC185" 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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185
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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186
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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;">pass</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -279,7 +280,7 @@ class SingleMatch(Match):</td>
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279
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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280
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span></span>
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281
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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282
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="s" style="color: #d14;"><span class="idiff left right">""</span></span><span class="p">,</span></span>
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">errors</span><span class="p">,</span></span>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstart</span><span class="p">,</span></span>
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rstop</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">@@ -381,6 +382,7 @@ class SingleAdapter(Adapter):</td>
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python"> <span class="n" style="color: #333;">indels</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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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="p">):</span></span>
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">remove</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="LC386" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_debug</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span> <span class="c1" style="color: #998; font-style: italic;"># type: bool</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_generate_adapter_name</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">name</span> <span class="c1" style="color: #998; font-style: italic;"># type: str</span></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">upper</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">"U"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># type: str</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -703,8 +705,16 @@ class MultiAdapter(Adapter):</td>
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_accept</span><span class="p">(</span><span class="n" style="color: #333;">adapter</span><span class="p">)</span></span>
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704
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706
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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="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">where</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_where</span><span class="p">:</span></span>
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707
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<pre style="margin: 0;"> <span id="LC707" 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;">"All adapters must have identical 'where' attributes"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_where</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">SUFFIX</span><span class="p">)</span></span>
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709
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_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="LC707" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_longest</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_index</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_lengths</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_index</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_index</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;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_where</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_affix</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">):</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">[:</span><span class="n" style="color: #333;">n</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC714" 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="LC715" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_affix</span><span class="p">(</span><span class="n" style="color: #333;">read</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="LC716" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="p">:]</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_make_affix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_affix</span></span>
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718
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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python"></span>
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709
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719
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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;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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710
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'MultiAdapter(adapters={!r}, where={})'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_where</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="751" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -741,7 +751,7 @@ class MultiAdapter(Adapter):</td>
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741
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751
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<pre style="margin: 0;"> <span id="LC751" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_make_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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742
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752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Building index of </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s adapters ...'</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters</span><span class="p">))</span></span>
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753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python"> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC744" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">ongest</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">engths</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">set</span></span><span class="p"><span class="idiff right">()</span></span></span>
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755
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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python"> <span class="n" style="color: #333;">has_warned</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters</span><span class="p">:</span></span>
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -762,35 +772,27 @@ class MultiAdapter(Adapter):</td>
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python"> <span class="n" style="color: #333;">has_warned</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="LC773" 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="LC774" class="line" lang="python"> <span class="n" style="color: #333;">index</span><span class="p">[</span><span class="n" style="color: #333;">s</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">adapter</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC765" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">ongest</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">max</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">longest</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="nb" style="color: #0086b3;">len</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="LC775" class="line" lang="python"> <span class="n" style="color: #333;">l<span class="idiff left">engths</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff right">(</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">))</span></span>
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Built an index containing </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s strings.'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">))</span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC768" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;"><span class="idiff left right">longest</span></span><span class="p">,</span> <span class="n" style="color: #333;">index</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">sorted</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">reverse</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">True</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="n" style="color: #333;">index</span></span>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC780" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match_to</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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<pre style="margin: 0;"> <span id="LC781" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="python"><span class="s" style="color: #d14;"> Match the adapters against the read and return a Match that represents</span></span>
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="python"><span class="s" style="color: #d14;"> the best match or None if no match was found</span></span>
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC775" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_where</span> <span class="ow" style="font-weight: 600;">is</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">PREFIX</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC776" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_affix</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="LC777" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">[:</span><span class="n" style="color: #333;">n</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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<pre style="margin: 0;">-<span id="LC779" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_affix</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="LC780" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">n</span><span class="p">:]</span></span>
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<pre style="margin: 0;">-<span id="LC781" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC782" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check all the prefixes of the read that could match</span></span>
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Check all the prefixes or suffixes (affixes) of the read that could match</span></span>
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="python"> <span class="n" style="color: #333;">best_adapter</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="LC787" class="line" lang="python"> <span class="n" style="color: #333;">best_length</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="LC788" class="line" lang="python"> <span class="n" style="color: #333;">best_m</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>
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"> <span class="n" style="color: #333;">best_e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1000</span></span>
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<pre style="margin: 0;">-<span id="LC787" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO do not go through all the lengths, only those that actually exist in the index</span></span>
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<pre style="margin: 0;">-<span id="LC788" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_longest</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</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;">for</span> <span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_lengths</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">best_m</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC792" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># No chance of getting the same or a higher number of matches, so we can stop early</span></span>
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<pre style="margin: 0;"> <span id="LC793" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC793" class="line" lang="python"> <span class="n" style="color: #333;">affix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">make_affix</span></span><span class="p"><span class="idiff right">(</span></span><span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="python"> <span class="n" style="color: #333;">affix</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_make_affix</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">length</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_index</span><span class="p">[</span><span class="n" style="color: #333;">affix</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">KeyError</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#6ed465db6839a69141086c2acf1dc01a8b17a981"><strong>src/cutadapt/filters.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,9 +13,13 @@ filters is created and each redirector is called in turn until one returns True.</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">The read is then assumed to have been "consumed", that is, either written</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">somewhere or filtered (should be discarded).</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">abc</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ABC</span><span class="p">,</span> <span class="n" style="color: #333;">abstractmethod</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">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="LC18" 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;">Match</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">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;">Tuple</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">Dict</span><span class="p">,</span> <span class="n" style="color: #333;">Any</span></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="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;">expected_errors</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">FileOpener</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ModificationInfo</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Constants used when returning from a Filter’s __call__ method to improve</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,81 +30,113 @@ KEEP = False</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndFilter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC32" 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="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</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;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="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;"> Called to process a single-end read</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;"> Any adapter matches are append to the matches list.</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedEndFilter</span><span class="p">(</span><span class="n" style="color: #333;">ABC</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC42" 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="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">matches1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">matches2</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">info1</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">,</span> <span class="n" style="color: #333;">info2</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;"> Called to process the read pair (read1, read2)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;"> Any adapter matches are append to the info.matches list.</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">WithStatistics</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="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-></span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># no. of written reads or read pairs</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Counter</span><span class="p">(),</span> <span class="n" style="color: #333;">Counter</span><span class="p">()]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[Counter]</span></span>
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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;">written_reads</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;">int</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written_bp</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="o" style="font-weight: 600;">...</span><span class="p">]:</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written_lengths</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;">Counter</span><span class="p">,</span> <span class="n" style="color: #333;">Counter</span><span class="p">]:</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(),</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">())</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndFilterWithStatistics</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">,</span> <span class="n" style="color: #333;">WithStatistics</span><span class="p">,</span> <span class="n" style="color: #333;">ABC</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update_statistics</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="bp" style="color: #999;">None</span><span class="p">:</span></span>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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37
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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38
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"></span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedEndFilterWithStatistics</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</span><span class="p">,</span> <span class="n" style="color: #333;">WithStatistics</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="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 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="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update_statistics</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">):</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read1</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_lengths</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">)]</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="LC87" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NoFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilterWithStatistics</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;"> No filtering, just send each read to the given writer.</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">writer</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</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 written reads TODO move to writer</span></span>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC48" 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="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filtered</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="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedNoFilter</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedNoFilter</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;"> No filtering, just send each paired-end read to the given writer.</span></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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107
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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">writer</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</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 written reads or read pairs TODO move to writer</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC68" 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="LC69" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">filtered</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="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">matches1</span><span class="p">,</span> <span class="n" style="color: #333;">matches2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;">info1</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">,</span> <span class="n" style="color: #333;">info2</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Redirector</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Redirector</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;"> Redirect discarded reads to the given writer. This is for single-end reads.</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">:</span> <span class="n" style="color: #333;">SingleEndFilter</span><span class="p">,</span> <span class="n" style="color: #333;">filter2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO filter2 should really not be here</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span></span>
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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="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">filter</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</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 written reads TODO move to writer</span></span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span></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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedRedirector</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedRedirector</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"><span class="s" style="color: #d14;"> Redirect paired-end reads matching a filtering criterion to a writer.</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"><span class="s" style="color: #d14;"> Different filtering styles are supported, differing by which of the</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -113,14 +149,13 @@ class PairedRedirector(PairedEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"><span class="s" style="color: #d14;"> 'both': The pair is discarded if both reads match.</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"><span class="s" style="color: #d14;"> 'first': The pair is discarded if the first read matches.</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pair_filter_mode</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'any'</span><span class="p">,</span> <span class="s" style="color: #d14;">'both'</span><span class="p">,</span> <span class="s" style="color: #d14;">'first'</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC154" 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;">"pair_filter_mode must be 'any', 'both' or 'first'"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">writer</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">filter</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filter2</span></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span> <span class="c1" style="color: #998; font-style: italic;"># no of written reads or read pairs TODO move to writer</span></span>
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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered_first</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">filter</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -132,26 +167,24 @@ class PairedRedirector(PairedEndFilter):</td>
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132
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered_first</span></span>
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_any</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filter2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_any</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filter2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filter2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_both</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">and</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">filter2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_first</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span>1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_first</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span>1</span><span class="p">)</span></span>
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143
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178
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<pre style="margin: 0;"> <span id="LC178" 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;">_is_filtered_second</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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145
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span>2</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_is_filtered_second</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filter2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span>2</span><span class="p">)</span></span>
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146
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">):</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_is_filtered</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">):</span></span>
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149
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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150
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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;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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151
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186
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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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152
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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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153
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read1</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">read2</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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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156
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -160,7 +193,7 @@ class TooShortReadFilter(SingleEndFilter):</td>
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160
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193
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">minimum_length</span><span class="p">):</span></span>
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161
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minimum_length</span></span>
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162
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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197
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">minimum_length</span></span>
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"></span>
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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<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>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -168,13 +201,29 @@ class TooLongReadFilter(SingleEndFilter):</td>
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168
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">maximum_length</span><span class="p">):</span></span>
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169
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maximum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maximum_length</span></span>
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203
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<pre style="margin: 0;"> <span id="LC203" 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;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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205
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maximum_length</span></span>
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173
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">MaximumExpectedErrorsFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> Discard reads whose expected number of errors, according to the quality</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;"> values, exceeds a threshold.</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> The idea comes from usearch's -fastq_maxee parameter</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"> (http://drive5.com/usearch/).</span></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC216" 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;">max_errors</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">max_errors</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">:</span> <span class="n" style="color: #333;">ModificationInfo</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="s" style="color: #d14;">"""Return True when the read should be discarded"""</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_errors</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"></span>
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175
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NContentFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">"""</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;"> Discard<span class="idiff left right">s a reads that has a number of 'N's over a given threshold</span>. It handles both raw counts</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"><span class="s" style="color: #d14;"> Discard<span class="idiff left right"> a read if it has too many 'N' bases</span>. It handles both raw counts</span></span>
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178
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="s" style="color: #d14;"> of Ns as well as proportions. Note, for raw counts, it is a 'greater than' comparison,</span></span>
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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;"> so a cutoff of '1' will keep reads with a single N in it.</span></span>
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,7 +236,7 @@ class NContentFilter(SingleEndFilter):</td>
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187
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_proportion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">1.0</span></span>
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188
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237
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span></span>
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189
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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191
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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;">"""Return True when the read should be discarded"""</span></span>
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192
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">n_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'n'</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_proportion</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -202,16 +251,16 @@ class DiscardUntrimmedFilter(SingleEndFilter):</td>
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202
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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203
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;"> Return True if read is untrimmed.</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">matches</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span></span>
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207
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">DiscardTrimmedFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"><span class="s" style="color: #d14;"> Return True if read is trimmed.</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"></span>
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CasavaFilter</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</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">@@ -222,12 +271,12 @@ class CasavaFilter(SingleEndFilter):</td>
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"></span>
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"><span class="s" style="color: #d14;"> Reads with unrecognized headers are kept.</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></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;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">right</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">partition</span><span class="p">(</span><span class="s" style="color: #d14;">' '</span><span class="p">)</span></span>
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227
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">right</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">':Y:'</span> <span class="c1" style="color: #998; font-style: italic;"># discard if :Y: found</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></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="LC230" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter</span><span class="p">):</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex trimmed reads. Reads are written to different output files</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="s" style="color: #d14;"> depending on which adapter matches. Files are created when the first read</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -240,35 +289,32 @@ class Demultiplexer(SingleEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;"> Reads without an adapter match are written to the file named by</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;"> untrimmed_path.</span></span>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'{name}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">path_template</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path_template</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">untrimmed_path</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities</span></span>
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>
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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"><span class="s" style="color: #d14;"> Write the read to the proper output file according to the most recent match</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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259
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<td class="diff-line-num new_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">:</span></span>
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260
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnaio_open_raise_limit</span><span class="p">(</span></span>
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261
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309
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name}'</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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262
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<pre style="margin: 0;">-<span id="LC262" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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264
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311
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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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265
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312
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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266
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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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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267
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314
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnaio_open_raise_limit</span><span class="p">(</span></span>
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268
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315
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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">)</span></span>
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269
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<td class="diff-line-num new_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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271
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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272
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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273
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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;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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<pre style="margin: 0;"> <span id="LC320" 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">@@ -279,7 +325,7 @@ class Demultiplexer(SingleEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_writer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex trimmed paired-end reads. Reads are written to different output files</span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"><span class="s" style="color: #d14;"> depending on which adapter (in read 1) matches.</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -292,34 +338,40 @@ class PairedDemultiplexer(PairedEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"><span class="s" style="color: #d14;"> Read pairs without an adapter match are written to the files named by</span></span>
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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"><span class="s" style="color: #d14;"> untrimmed_path.</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_path</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_paired_path</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC300" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written</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="LC301" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written</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;">int</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span> <span class="o" style="font-weight: 600;">+</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written</span></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="python"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>
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<pre style="margin: 0;">-<span id="LC304" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written_bp</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="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</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="LC349" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">written_bp</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="LC350" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_written_bp</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="LC351" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">read2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC309" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span>1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span>1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span>1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span>1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC357" 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="LC358" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC317" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CombinatorialDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter</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;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CombinatorialDemultiplexer</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndFilter<span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"><span class="s" style="color: #d14;"> Demultiplex reads depending on which adapter matches, taking into account both matches</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"><span class="s" style="color: #d14;"> on R1 and R2.</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="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">path_template</span><span class="p">,</span> <span class="n" style="color: #333;">path_paired_template</span><span class="p">,</span> <span class="n" style="color: #333;">untrimmed_name</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="n" style="color: #333;">file_opener</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC367" 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="LC368" 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="LC369" class="line" lang="python"> <span class="n" style="color: #333;">path_template</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="LC370" class="line" lang="python"> <span class="n" style="color: #333;">path_paired_template</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="LC371" class="line" lang="python"> <span class="n" style="color: #333;">untrimmed_name</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>
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">qualities</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="LC373" class="line" lang="python"> <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="LC374" class="line" lang="python"> <span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"><span class="s" style="color: #d14;"> path_template must contain the string '{name1}' and '{name2}', which will be replaced</span></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;"> with the name of the adapters found on R1 and R2, respectively to form the final output</span></span>
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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">@@ -327,15 +379,17 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"><span class="s" style="color: #d14;"> specified by untrimmed_name. Alternatively, untrimmed_name can be set to None; in that</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"><span class="s" style="color: #d14;"> case, read pairs for which at least one read does not have an adapter match are</span></span>
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"><span class="s" style="color: #d14;"> discarded.</span></span>
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="python"><span class="s" style="color: #d14;"> untrimmed_name -- what to replace the templates with when one or both of the reads</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="python"><span class="s" style="color: #d14;"> do not contain an adapter (use "unknown"). Set to None to discard these read pairs.</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'{name1}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">path_template</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'{name2}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">path_template</span></span>
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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">'{name1}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">path_paired_template</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'{name2}'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">path_paired_template</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path_template</span></span>
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired_template</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path_paired_template</span></span>
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391
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">untrimmed_name</span></span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># type: Dict[Tuple[str, str], Any]</span></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities</span></span>
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_opener</span></span>
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<pre style="margin: 0;"> <span id="LC395" 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">@@ -343,16 +397,17 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_make_path</span><span class="p">(</span><span class="n" style="color: #333;">template</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name1}'</span><span class="p">,</span> <span class="n" style="color: #333;">name1</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name2}'</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC402" class="line" lang="python"><span class="s" style="color: #d14;"> Write the read to the proper output file according to the most recent matches both on</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"><span class="s" style="color: #d14;"> R1 and R2</span></span>
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">read2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="python"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches1</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC353" class="line" lang="python"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">matches2</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="python"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">matches</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="python"> <span class="n" style="color: #333;">name2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">info2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">matches</span></span> <span class="k" style="font-weight: 600;">else</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Open writer on first use</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="n" style="color: #333;">name1</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">untrimmed_name</span></span>
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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -366,9 +421,7 @@ class CombinatorialDemultiplexer(PairedEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC421" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">file_opener</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dnaio_open_raise_limit</span><span class="p">(</span><span class="n" style="color: #333;">path2</span><span class="p">,</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="n" style="color: #333;">writer1</span><span class="p">,</span> <span class="n" style="color: #333;">writer2</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">writers</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC369" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span><span class="p">[</span><span class="mi" style="color: #099;">1</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;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="n" style="color: #333;">writer1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"> <span class="n" style="color: #333;">writer2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">DISCARD</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -383,9 +436,10 @@ class RestFileWriter(SingleEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO this fails with linked adapters</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="n" style="color: #333;">rest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rest</span><span class="p">()</span></span>
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389
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443
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rest</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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390
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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">rest</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="449" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -395,9 +449,10 @@ class WildcardFileWriter(SingleEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcards</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">info</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO this fails with linked adapters</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wildcards</span><span class="p">(),</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">KEEP</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC458" 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">@@ -405,11 +460,12 @@ class InfoFileWriter(SingleEndFilter):</td>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC408" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">List</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Match</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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<pre style="margin: 0;">-<span id="LC409" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">info_record</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_info_records</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC412" 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;">info_record</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># info_record[0] is the read name suffix</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">info_record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">:],</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">file</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC469" 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="LC470" class="line" lang="python"> <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python"> <span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">''</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#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">@@ -13,15 +13,27 @@ from .adapters import Where, MultiAdapter, Match, remainder</td>
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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;">.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="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Modifier</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="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ModificationInfo</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;"> An object of this class is created for each read that passes through the pipeline.</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;"> Any information (except the read itself) that needs to be passed from one modifier</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;"> to one later in the pipeline or from one modifier to the filters is recorded here.</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="n" style="color: #333;">__slots__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"matches"</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[Match]</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SingleEndModifier</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="LC29" 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="LC18" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">List</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Match</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedModifier</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="LC35" 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="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></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;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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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">@@ -31,24 +43,26 @@ class PairedModifierWrapper(PairedModifier):</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">paired</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC34" 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;">modifier1</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">Modifier</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">modifier2</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 right">[</span></span><span class="n" style="color: #333;">Modifier</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC46" 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;">modifier1</span><span class="p">:</span> <span class="n" style="color: #333;">Optional</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left">SingleEndModifier</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">modifier2</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="n" style="color: #333;"><span class="idiff right">SingleEnd</span>Modifier</span><span class="p">]):</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"""Set one of the modifiers to None to work on R1 or R2 only"""</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier1</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier2</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC51" 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 may be None"</span><span class="p">)</span></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;">__repr__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'PairedModifier(modifier1={!r}, modifier2={!r})'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</span><span class="p">)</span></span>
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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="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches2</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ModificationInfo</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info2</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches2</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info2</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># type: ignore</span></span></span>
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46
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier2</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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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span>1</span><span class="p">),</span> <span class="n" style="color: #333;">read2</span></span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_modifier2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span>1</span><span class="p">),</span> <span class="n" style="color: #333;">read2</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifier1</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">),</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_modifier2</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">read2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterCutter</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="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">AdapterCutter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"><span class="s" style="color: #d14;"> Repeatedly find one of multiple adapters in reads.</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"><span class="s" style="color: #d14;"> The number of times the search is repeated is specified by the</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -148,13 +162,13 @@ class AdapterCutter(Modifier):</td>
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148
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span></span>
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149
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trimmed_read</span></span>
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150
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164
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<pre style="margin: 0;"> <span id="LC164" 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 class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">in<span class="idiff left">matches</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">List</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Match</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">in<span class="idiff left">fo</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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152
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166
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_and_trim</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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153
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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154
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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155
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>
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156
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_statistics</span><span class="p">[</span><span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="p">])</span></span>
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157
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">in<span class="idiff left">matches</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">in<span class="idiff left">fo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># TODO extend or overwrite?</span></span></span>
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158
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trimmed_read</span></span>
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159
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"></span>
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160
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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<td class="diff-line-num unfold js-unfold old_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="diff-line-num unfold js-unfold new_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -198,7 +212,7 @@ class AdapterCutter(Modifier):</td>
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198
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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199
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ReverseComplementer</span><span class="p">(</span><span class="n" style="color: #333;">Modifier</span><span class="p">):</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ReverseComplementer</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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202
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"""Trim adapters from a read and its reverse complement"""</span></span>
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"></span>
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204
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">adapter_cutter</span><span class="p">:</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">,</span> <span class="n" style="color: #333;">rc_suffix</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;">" rc"</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -209,7 +223,7 @@ class ReverseComplementer(Modifier):</td>
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209
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reverse_complemented</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="LC224" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rc_suffix</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">in<span class="idiff left">matches</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">List</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Match</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">in<span class="idiff left">fo</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"> <span class="n" style="color: #333;">reverse_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_complemented_sequence</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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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 class="n" style="color: #333;">forward_trimmed_read</span><span class="p">,</span> <span class="n" style="color: #333;">forward_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_cutter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_and_trim</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); 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="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -234,7 +248,7 @@ class ReverseComplementer(Modifier):</td>
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248
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<pre style="margin: 0;"> <span id="LC248" 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;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_cutter</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;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python"> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update_statistics</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">stats</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">reverse_complemented</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="n" style="color: #333;">use_reverse_complement</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">in<span class="idiff left">matches</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">in<span class="idiff left">fo</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">extend</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># TODO extend or overwrite?</span></span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">trimmed_read</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -277,7 +291,7 @@ class PairedAdapterCutter(PairedModifier):</td>
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">'PairedAdapterCutter(adapters1={!r}, adapters2={!r})'</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters1</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"> <span class="n" style="color: #333;">match1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">best_match</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_adapters1</span><span class="p">,</span> <span class="n" style="color: #333;">read1</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">@@ -310,12 +324,12 @@ class PairedAdapterCutter(PairedModifier):</td>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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="LC325" 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="LC326" class="line" lang="python"> <span class="n" style="color: #333;">result</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">trimmed_read</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">matches1</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match1</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">matches2</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">matches</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">info2</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">matches</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span></span>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC318" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">UnconditionalCutter</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="LC332" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">UnconditionalCutter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"><span class="s" style="color: #d14;"> A modifier that unconditionally removes the first n or the last n bases from a read.</span></span>
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<pre style="margin: 0;"> <span id="LC335" 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">@@ -325,14 +339,14 @@ class UnconditionalCutter(Modifier):</td>
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<pre style="margin: 0;"> <span id="LC339" 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;">length</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="LC340" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">List</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">Match</span></span><span class="p"><span class="idiff right">]</span>):</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC344" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">:]</span></span>
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC346" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LengthTagModifier</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="LC349" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">LengthTagModifier</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"><span class="s" style="color: #d14;"> Replace "length=..." strings in read names.</span></span>
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<pre style="margin: 0;"> <span id="LC352" 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">@@ -340,28 +354,28 @@ class LengthTagModifier(Modifier):</td>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">regex</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r"\b"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">length_tag</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">r"[0-9]*\b"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length_tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length_tag</span></span>
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python"> <span class="n" style="color: #333;">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="LC359" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length_tag</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">regex</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sub</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length_tag</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">)),</span> <span class="n" style="color: #333;">read</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="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC350" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SuffixRemover</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="LC364" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SuffixRemover</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"><span class="s" style="color: #d14;"> Remove a given suffix from read names.</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC368" 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;">suffix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suffix</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="n" style="color: #333;">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="LC373" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suffix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suffix</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span></span>
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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PrefixSuffixAdder</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="LC378" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PrefixSuffixAdder</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"><span class="s" style="color: #d14;"> Add a suffix and a prefix to read names</span></span>
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<pre style="margin: 0;"> <span id="LC381" 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">@@ -369,15 +383,15 @@ class PrefixSuffixAdder(Modifier):</td>
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prefix</span></span>
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suffix</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">suffix</span></span>
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"> <span class="n" style="color: #333;">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="LC374" class="line" lang="python"> <span class="n" style="color: #333;">adapter_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">matches</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">matches</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'no_adapter'</span></span>
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="python"> <span class="n" style="color: #333;">adapter_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">matches</span></span><span class="p"><span class="idiff">[</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">adapter</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">name</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">info</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></span><span class="n" style="color: #333;">matches</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'no_adapter'</span></span>
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name}'</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">+</span> \</span>
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'{name}'</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span></span>
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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC380" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ZeroCapper</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="LC394" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ZeroCapper</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python"><span class="s" style="color: #d14;"> Change negative quality values of a read to zero</span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -385,38 +399,38 @@ class ZeroCapper(Modifier):</td>
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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python"> <span class="n" style="color: #333;">qb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quality_base</span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zero_cap_trans</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maketrans</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">qb</span><span class="p">))),</span> <span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">qb</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">qb</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python"> <span class="n" style="color: #333;">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="LC404" class="line" lang="python"> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">translate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">zero_cap_trans</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">read</span></span>
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NextseqQualityTrimmer</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="LC408" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NextseqQualityTrimmer</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC409" 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;">cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="p">):</span></span>
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutoff</span></span>
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span></span>
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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">trimmed_bases</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="LC413" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></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;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"> <span class="n" style="color: #333;">stop</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nextseq_trim_index</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">base</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">trimmed_bases</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 class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">stop</span></span>
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<pre style="margin: 0;"> <span id="LC417" 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;">stop</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC406" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">QualityTrimmer</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="LC420" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">QualityTrimmer</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff_front</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff_back</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff_front</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutoff_front</span></span>
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<pre style="margin: 0;"> <span id="LC423" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff_back</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutoff_back</span></span>
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">base</span></span>
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">trimmed_bases</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="LC426" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC413" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python"> <span class="n" style="color: #333;">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;">quality_trim_index</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff_front</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cutoff_back</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">base</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">trimmed_bases</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 class="o" style="font-weight: 600;">-</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;">start</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC419" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Shortener</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="LC433" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Shortener</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"> <span class="s" style="color: #d14;">"""Unconditionally shorten a read to the given length</span></span>
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;"> If the length is positive, the bases are removed from the end of the 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">@@ -425,20 +439,20 @@ class Shortener(Modifier):</td>
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<pre style="margin: 0;"> <span id="LC439" 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;">length</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">length</span></span>
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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python"></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;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC444" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC445" 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="LC446" 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="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</span><span class="p">:]</span></span>
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<pre style="margin: 0;"> <span id="LC447" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NEndTrimmer</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="LC449" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NEndTrimmer</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"> <span class="s" style="color: #d14;">"""Trims Ns from the 3' and 5' end of reads"""</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'^N+'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_trim</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">r'N+$'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python"> <span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python"> <span class="n" style="color: #333;">start_cut</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">start_trim</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python"> <span class="n" style="color: #333;">end_cut</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">end_trim</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">search</span><span class="p">(</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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<li id="1b86cdea057b59b4d05ba7fde4aea9df4e8fe9e8">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#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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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">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;">IO</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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">Union</span></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;">IO</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>
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8
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8
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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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9
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9
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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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10
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10
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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">@@ -16,10 +16,11 @@ from xopen import xopen</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">dnaio</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.utils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Progress</span><span class="p">,</span> <span class="n" style="color: #333;">FileOpener</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">Modifier</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedModifier</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">PairedModifierWrapper</span></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;"><span class="idiff left">SingleEndModifier</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedModifier</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedModifierWrapper</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.report</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Statistics</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.filters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Redirector</span><span class="p">,</span> <span class="n" style="color: #333;">PairedRedirector</span><span class="p">,</span> <span class="n" style="color: #333;">NoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedNoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFileWriter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">RestFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">TooShortReadFilter</span><span class="p">,</span> <span class="n" style="color: #333;">TooLongReadFilter</span><span class="p">,</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">MaximumExpectedErrorsFilter</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="n" style="color: #333;">CasavaFilter</span><span class="p">,</span> <span class="n" style="color: #333;">DiscardTrimmedFilter</span><span class="p">,</span> <span class="n" style="color: #333;">DiscardUntrimmedFilter</span><span class="p">,</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">PairedDemultiplexer</span><span class="p">,</span> <span class="n" style="color: #333;">CombinatorialDemultiplexer</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" 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">@@ -98,10 +99,8 @@ class Pipeline(ABC):</td>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span 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="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_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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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># type: Any</span></span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_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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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO type should be Union[List[Modifier], List[PairedModifier]]</span></span>
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104
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[Union[Modifier, PairedModifier]]</span></span>
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105
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_outfiles</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[OutputFiles]</span></span>
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106
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_demultiplexer</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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107
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[TextIO]</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -110,6 +109,7 @@ class Pipeline(ABC):</td>
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110
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_minimum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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111
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_maximum_length</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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112
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_expected_errors</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_casava</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_trimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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115
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_untrimmed</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); 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="172" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -172,6 +172,13 @@ class Pipeline(ABC):</td>
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172
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172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_n</span><span class="p">)</span></span>
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173
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">))</span></span>
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174
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_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 new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">delivers_qualities</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Ignoring option --max-ee as input does not contain quality values"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">MaximumExpectedErrorsFilter</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_expected_errors</span><span class="p">)</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">))</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="python"></span>
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">discard_casava</span><span class="p">:</span></span>
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176
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">f1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CasavaFilter</span><span class="p">()</span></span>
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177
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">filter_wrapper</span><span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">f1</span><span class="p">,</span> <span class="n" style="color: #333;">f2</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="218" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -211,6 +218,7 @@ class Pipeline(ABC):</td>
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211
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">flush</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC220" 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="LC221" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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214
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_textiowrappers</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># This also closes the underlying files; a second close occurs below</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -255,9 +263,9 @@ class SingleEndPipeline(Pipeline):</td>
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC264" 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="LC265" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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258
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<pre style="margin: 0;">-<span id="LC258" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span><span class="idiff left"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right"># type: List[SingleEndModifier]</span></span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"></span>
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260
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<pre style="margin: 0;">-<span id="LC260" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">:</span> <span class="n" style="color: #333;">Modifier</span><span class="p">):</span></span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">modifier</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left right">SingleEnd</span>Modifier</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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">modifier</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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262
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="k" style="font-weight: 600;">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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263
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271
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">modifier</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -271,12 +279,12 @@ class SingleEndPipeline(Pipeline):</td>
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271
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279
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<pre style="margin: 0;"> <span id="LC279" 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;">1</span></span>
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272
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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;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10000</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">progress</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"> <span class="n" style="color: #333;">progress</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">total_bp</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="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">sequence</span></span><span class="p">)</span></span>
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275
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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">matches</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="python"> <span class="n" style="color: #333;">total_bp</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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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">info</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">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span></span></span>
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276
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">modifier</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">:</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span></span><span class="p">)</span></span>
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278
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filter_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</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;">if</span> <span class="n" style="color: #333;">filter_</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">matches</span></span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter_</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">info</span></span><span class="p">):</span></span>
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280
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">total_bp</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="330" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -322,12 +330,13 @@ class PairedEndPipeline(Pipeline):</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">pair_filter_mode</span><span class="p">,</span> <span 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="LC332" class="line" lang="python"> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">file_opener</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[PairedModifier]</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pair_filter_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pair_filter_mode</span></span>
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;"> <span id="LC336" 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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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">override_untrimmed_pair_filter</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC330" 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;"><span class="idiff left">Modifier</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">modifier2</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 right">[</span></span><span class="n" style="color: #333;">Modifier</span><span class="p">]):</span></span>
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<pre style="margin: 0;">+<span id="LC339" 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;"><span class="idiff left">SingleEndModifier</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">modifier2</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="n" style="color: #333;"><span class="idiff right">SingleEnd</span>Modifier</span><span class="p">]):</span></span>
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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC341" 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="LC342" 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">@@ -336,7 +345,7 @@ class PairedEndPipeline(Pipeline):</td>
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<pre style="margin: 0;"> <span id="LC345" 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="LC346" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">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="LC347" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;">Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="python"> <span class="k" style="font-weight: 600;">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;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC350" 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="LC351" 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">@@ -356,15 +365,15 @@ class PairedEndPipeline(Pipeline):</td>
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<pre style="margin: 0;"> <span id="LC365" 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;">1</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">%</span> <span class="mi" style="color: #099;">10000</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">progress</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"> <span class="n" style="color: #333;">progress</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC359" class="line" lang="python"> <span class="n" style="color: #333;">total1_bp</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;">read1</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">sequence</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"> <span class="n" style="color: #333;">total2_bp</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;">read2</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff right">sequence</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">matches2</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">[]</span></span></span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">total1_bp</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;">read1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">total2_bp</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;">read2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">info1</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">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">info2</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">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">modifier</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_modifiers</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC364" class="line" lang="python"> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">modifier</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC374" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filter_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filters</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC375" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Stop writing as soon as one of the filters was successful.</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter_</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">matches1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">matches</span>2</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">filter_</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">info1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">info</span>2</span><span class="p">):</span></span>
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368
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377
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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"> <span class="k" style="font-weight: 600;">break</span></span>
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369
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</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>
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370
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -556,7 +565,6 @@ class WorkerProcess(Process):</td>
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556
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565
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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"> <span class="n" style="color: #333;">orig_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">getattr</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_orig_outfiles</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">)</span></span>
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557
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566
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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">orig_outfile</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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558
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567
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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python"> <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">io</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BytesIO</span><span class="p">()</span></span>
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559
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">orig_outfile</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">name</span></span>
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560
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568
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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python"> <span class="nb" style="color: #0086b3;">setattr</span><span class="p">(</span><span class="n" style="color: #333;">output_files</span><span class="p">,</span> <span class="n" style="color: #333;">attr</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">)</span></span>
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561
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569
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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"></span>
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570
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">output_files</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -602,7 +610,7 @@ class PipelineRunner(ABC):</td>
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python"><span class="s" style="color: #d14;"> A read processing pipeline</span></span>
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604
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612
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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC605" 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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613
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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;">__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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606
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614
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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_pipeline</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pipeline</span></span>
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607
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615
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_progress</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">progress</span></span>
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608
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -614,6 +622,12 @@ class PipelineRunner(ABC):</td>
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<pre style="margin: 0;"> <span id="LC622" 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="LC623" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</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="LC626" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python"></span>
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ParallelPipelineRunner</span><span class="p">(</span><span class="n" style="color: #333;">PipelineRunner</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<li id="5a4a773b73e0bdb43c051d1b039d337cd428e3e1">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#5a4a773b73e0bdb43c051d1b039d337cd428e3e1"><strong>src/cutadapt/qualtrim.pyx</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">@@ -82,3 +82,25 @@ def nextseq_trim_index(sequence, int cutoff, int base=33):</td>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cython"> <span class="n" style="color: #333;">max_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cython"> <span class="n" style="color: #333;">max_i</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">max_i</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cython"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">expected_errors</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">str</span> <span class="n" style="color: #333;">qualities</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cython"><span class="s" style="color: #d14;"> Return the number of expected errors (as double) from a read’s</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cython"><span class="s" style="color: #d14;"> qualities.</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cython"><span class="s" style="color: #d14;"> This uses the formula in Edgar et al. (2015),</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cython"><span class="s" style="color: #d14;"> see Section 2.2 in <https://academic.oup.com/bioinformatics/article/31/21/3476/194979>.</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cython"><span class="s" style="color: #d14;"> qualities -- ASCII-encoded qualities (chr(qual + base))</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">q</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">quals</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qualities</span><span class="o" style="font-weight: 600;">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">quals</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cython"></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cython"> <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="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">qualities</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="cython"> <span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cq</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;">base</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cython"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">**</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">/</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">e</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -3,13 +3,12 @@ Routines for printing a report.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">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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<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;">textwrap</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;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Counter</span></span>
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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;">typing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Any</span><span class="p">,</span> <span class="n" style="color: #333;">Optional</span><span class="p">,</span> <span class="n" style="color: #333;">List</span></span>
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7
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">EndStatistics</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterStatistics</span><span class="p">,</span> <span class="n" style="color: #333;">ADAPTER_TYPE_NAMES</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;">.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">Modifier</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="LC9" 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;"><span class="idiff left right">SingleEnd</span>Modifier</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="LC10" 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="LC10" 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;">NoFilter</span><span class="p">,</span> <span class="n" style="color: #333;">PairedNoFilter</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>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">PairedDemultiplexer</span><span class="p">,</span> <span class="n" style="color: #333;">CombinatorialDemultiplexer</span><span class="p">,</span> <span class="n" style="color: #333;">Demultiplexer</span><span class="p">,</span> <span class="n" style="color: #333;">NContentFilter</span><span class="p">,</span> <span class="n" style="color: #333;">InfoFileWriter</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">WildcardFileWriter</span><span class="p">,</span> <span class="n" style="color: #333;">RestFileWriter</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.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="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="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">@@ -41,6 +40,7 @@ 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">total_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Counter</span><span class="p">(),</span> <span class="n" style="color: #333;">Counter</span><span class="p">()]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[Counter]</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quality_trimmed_bp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[],</span> <span class="p">[]]</span> <span class="c1" style="color: #998; font-style: italic;"># type: List[List[AdapterStatistics]]</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,6 +66,7 @@ class Statistics:</td>
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<pre style="margin: 0;"> <span id="LC66" 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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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="o" style="font-weight: 600;">.</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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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">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="o" style="font-weight: 600;">.</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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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_lengths</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">written_lengths</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span></span>
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69
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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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</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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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quality_trimmed_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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quality_trimmed_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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72
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_stats</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">adapter_stats</span><span class="p">[</span><span class="n" style="color: #333;">i</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">@@ -102,13 +103,13 @@ class Statistics:</td>
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102
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>
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103
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>
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104
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_collect_writer</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">w</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;">if</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="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">InfoFileWriter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">RestFileWriter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">WildcardFileWriter</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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106
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left right">return</span></span></span>
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107
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">elif</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">isinstance</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">w</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">NoFilter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedNoFilter</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">PairedDemultiplexer</span></span><span class="p"><span class="idiff right">,</span></span></span>
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108
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">CombinatorialDemultiplexer</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">Demultiplexer</span></span><span class="p"><span class="idiff right">)):</span></span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">written</span></span></span>
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110
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<pre style="margin: 0;">-<span id="LC110" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff">[</span></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="LC111" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="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;">w</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">WithStatistics</span></span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_reads</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">written_bp</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">written_lengths</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">w</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_lengths</span></span><span class="p"><span class="idiff right">()</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">:</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_bp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">written_bp</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></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="idiff left"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">written_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</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">written_lengths</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">]</span></span>
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112
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113
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<pre style="margin: 0;"> <span id="LC113" 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="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">TooShortReadFilter</span><span class="p">):</span></span>
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113
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_short</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span></span>
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114
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">,</span> <span class="n" style="color: #333;">TooLongReadFilter</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,7 +117,7 @@ class Statistics:</td>
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116
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">.</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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117
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">too_many_n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filtered</span></span>
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118
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"></span>
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119
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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_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;">Modifier</span><span class="p">):</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"> <span class="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;"><span class="idiff left right">SingleEnd</span>Modifier</span><span class="p">):</span></span>
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120
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121
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<pre style="margin: 0;"> <span id="LC121" 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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121
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</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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122
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</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;">m</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">with_adapters</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -368,7 +369,7 @@ def full_report(stats: Statistics, time: float, gc_content: float) -> str: # no</td>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="python"> <span class="n" style="color: #333;">print_s</span><span class="p">(</span><span class="s" style="color: #d14;">"Sequence: {}; Type: {}; Length: {}; Trimmed: {} times"</span><span class="o" style="font-weight: 600;">.</span></span>
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="python"> <span class="nb" style="color: #0086b3;">format</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;">front</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">ADAPTER_TYPE_NAMES</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;">where</span><span class="p">],</span></span>
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371
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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python"> <span class="nb" style="color: #0086b3;">len</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;">front</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">),</span> <span class="n" style="color: #333;">total</span><span class="p">),</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC371" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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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<pre style="margin: 0;">+<span id="LC372" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">stats</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">.</span></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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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python"> <span class="n" style="color: #333;">print_s</span><span class="p">(</span><span class="s" style="color: #d14;">"; Reverse-complemented: {} times"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">reverse_complemented</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC374" 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="LC375" class="line" lang="python"> <span class="n" style="color: #333;">print_s</span><span class="p">()</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#f1290ccc2d6eec0bb1ad5edec40935fde2e76d6d"><strong>tests/cut/maxee.fastq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@empty</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">@ee_0.8</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ACGTTGCA</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">++++++++</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#52341cb116c436b2626aa6ee2671f055508dcadd"><strong>tests/data/SRR2040271_1.fastq</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@SRR2040271.1 SN603_WBP007_8_1101_63.30_99.90 length=100</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">NTCATTCCATGACATTGTCTGTTGGTTGCTTTTTGAGTATATTTTCTCATGGCTTCATCTATCTTGCTCATAAGACTAAATGGGGAGACAGACTTCCTGG</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">+SRR2040271.1 SN603_WBP007_8_1101_63.30_99.90 length=100</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">!1=DDFFFGHHHHIJJJJJIIJJJGGHJGJIJJGBGGHEGHJIIIIEHIJEH>@G;FHCG<<BCG:CG@F4@D@=@DG>EE>EED(,,(;((,;;@A>CC</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">@SRR2040271.2 SN603_WBP007_8_1101_79.90_99.30 length=100</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">NTAAAGACCCTTCAACTCAGGGCTTCTGAACCCTGGCTACCCATTAGAATCACTTAGGGAGCTTTGAAAAATATCAACACCCCAGCCCTAACCCAGCCCA</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">+SRR2040271.2 SN603_WBP007_8_1101_79.90_99.30 length=100</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">!4=BBDDDFHHHH@FHIIIIIIIIIGIIHGIIIIIIIIHIIIIIICEGGIIIIIIGHIIEGHIGIIIHHHFHEEEEEEECC=B=@BBBCCCBBBBA(88?</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#b397851f95cdd4c047a24eda3a5a0cd99f8c755f"><strong>tests/data/maxee.fastq</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@empty</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">+</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">@ee_1</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">A</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">+</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">!</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">@ee_0.8</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">ACGTTGCA</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">+</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">++++++++</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">@ee_1.01</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">TGGACGTTGCA</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">+</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">+5+++++++++</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#9289ad7183fa284327eb87184ee37b941ba6e3e0"><strong>tests/data/plus.fastq</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@first_sequence some other text</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">SEQUENCE1</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">+first_sequence some other text</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">:6;;8<=:<</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">@second_sequence and more text</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">SEQUENCE2</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">+second_sequence and more text</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">83<??:(61</span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#4c91f80a781e5621e92c74fdd1bddaa8ef6b43e7"><strong>tests/test_adapters.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">-<span id="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;">SingleAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">SingleMatch</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span></span>
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<pre style="margin: 0;">+<span id="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;">SingleAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">SingleMatch</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">WhereToRemove</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue_52</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleAdapter</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;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'GAACTCCAGTCACNNNNN'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'suffix'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">WhereToRemove</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">SUFFIX</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.12</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;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</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;">read_wildcards</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +45,7 @@ def test_issue_80():</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleAdapter</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;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"TCGTATGCCGTCTTC"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'suffix'</span></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;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">WhereToRemove</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">SUFFIX</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">min_overlap</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"> <span class="n" style="color: #333;">read_wildcards</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,7 +58,7 @@ def test_issue_80():</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_str</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGT'</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'suffix'</span></span><span class="p">,</span> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">'ACGT'</span><span class="p">,</span> <span class="n" style="color: #333;">where</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span> <span class="n" style="color: #333;">remove</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">WhereToRemove</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">SUFFIX</span></span><span class="p">,</span> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_to</span><span class="p">(</span><span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'seq'</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'TTACGT'</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +91,7 @@ def test_info_record():</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">am</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SingleMatch</span><span class="p">(</span><span class="n" style="color: #333;">astart</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">astop</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">17</span><span class="p">,</span> <span class="n" style="color: #333;">rstart</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">rstop</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">21</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">remove_before</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="LC92" class="line" lang="python"> <span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">adapter</span><span class="p">,</span> <span class="n" style="color: #333;">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="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">am</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_info_records</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="LC94" class="line" lang="python"> <span class="s" style="color: #d14;">"<span class="idiff left right">abc</span>"</span><span class="p">,</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 class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="mi" style="color: #099;">2</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="mi" style="color: #099;">5</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python"> <span class="mi" style="color: #099;">21</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#83ff0d8e113228f36b352922cbbb938d0aa9384b"><strong>tests/test_commandline.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,7 +9,7 @@ import pytest</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</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;">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="LC12" 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 class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">redirect_stderr</span></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;">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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># pytest.mark.timeout will not fail even if pytest-timeout is not installed</span></span>
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<pre style="margin: 0;"> <span id="LC15" 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">@@ -69,19 +69,6 @@ def test_discard_untrimmed(run):</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">'-b CAAGAT --discard-untrimmed'</span><span class="p">,</span> <span class="s" style="color: #d14;">'discard-untrimmed.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Regression since switching to dnaio'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_second_header_retained</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="LC74" class="line" lang="python"> <span class="s" style="color: #d14;">"""test if sequence name after the "+" is retained"""</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--cores {} -e 0.12 -b TTAGACATATCTCCGTCG"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"plus.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"plus.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Regression since switching to dnaio'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_length_tag_second_header</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="LC80" class="line" lang="python"> <span class="s" style="color: #d14;">"""Ensure --length-tag= also modifies the second header line"""</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--cores {} -a GGCTTC --length-tag=length="</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"> <span class="s" style="color: #d14;">'SRR2040271_1.fastq'</span><span class="p">,</span> <span class="s" style="color: #d14;">'SRR2040271_1.fastq'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_extensiontxtgz</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="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"""automatic recognition of "_sequence.txt.gz" extension"""</span></span>
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<pre style="margin: 0;"> <span id="LC74" 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;">"s_1_sequence.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"s_1_sequence.txt.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">@@ -343,8 +330,16 @@ def test_adapter_with_u(run):</td>
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-a GCCGAACUUCUUAGACUGCCUUAAGGACGU"</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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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_bzip2</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="LC347" 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;">'small.fastq.bz2'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_bzip2_input</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="LC334" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span> <span class="s" style="color: #d14;">"-a"</span><span class="p">,</span> <span class="s" style="color: #d14;">"TTAGACATATCTCCGTCG"</span><span class="p">],</span> <span class="s" style="color: #d14;">"small.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"small.fastq.bz2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"extension"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"bz2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"xz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gz"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_compressed_output</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span><span class="p">,</span> <span class="n" style="color: #333;">cores</span><span class="p">,</span> <span class="n" style="color: #333;">extension</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC339" 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;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="s" style="color: #d14;">"small.fastq."</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extension</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;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC341" 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 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="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="LC342" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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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>
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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;">sys</span><span class="o" style="font-weight: 600;">.</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;">3</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -358,14 +353,12 @@ def test_xz(run):</td>
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_args</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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC361" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"> <span class="n" style="color: #333;">main</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;">main</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>
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_two_fastqs</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'paired.1.fastq'</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'paired.2.fastq'</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'paired.1.fastq'</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'paired.2.fastq'</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python"></span>
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anchored_no_indels</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="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -386,8 +379,7 @@ def test_anchored_no_indels_wildcard_adapt(run):</td>
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386
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379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"></span>
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387
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_non_iupac_characters</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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388
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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390
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<pre style="margin: 0;">-<span id="LC390" 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;">'ZACGT'</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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382
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<pre style="margin: 0;">+<span id="LC382" 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;">'ZACGT'</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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391
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383
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="python"></span>
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392
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="python"></span>
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393
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unconditional_cut_front</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="536" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -544,20 +536,17 @@ def test_linked_info_file(tmpdir):</td>
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544
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536
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<pre style="margin: 0;"> <span id="LC536" class="line" lang="python"></span>
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545
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_linked_anywhere</span><span class="p">():</span></span>
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546
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538
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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547
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<pre style="margin: 0;">-<span id="LC547" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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548
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<pre style="margin: 0;">-<span id="LC548" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AAA...TTT'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked.fasta'</span><span class="p">)])</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AAA...TTT'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'linked.fasta'</span><span class="p">)])</span></span>
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549
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540
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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"></span>
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550
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541
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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"></span>
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551
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542
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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anywhere_anchored_5p</span><span class="p">():</span></span>
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552
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543
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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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553
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<pre style="margin: 0;">-<span id="LC553" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'^AAA'</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="LC544" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'^AAA'</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="LC545" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC547" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_anywhere_anchored_3p</span><span class="p">():</span></span>
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC559" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC560" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TTT$'</span><span class="p">,</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">'small.fastq'</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">'-b'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TTT$'</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="LC550" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC551" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_fasta</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">@@ -709,15 +698,41 @@ def test_adapter_order(run):</td>
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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"-a CCGGG -g ^AAACC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapterorder-ag.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapterorder.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC699" class="line" lang="python"></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="LC712" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">skip</span><span class="p">(</span><span class="n" style="color: #333;">reason</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Not implemented"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC713" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_complement_not_normalized</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="LC714" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span><span class="s" style="color: #d14;">"--rc=yes -g ^TTATTTGTCT -g ^TCCGCACTGG"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">"revcomp-notnormalized-single.fastq"</span><span class="p">,</span> <span class="s" style="color: #d14;">"revcomp.1.fastq"</span><span class="p">)</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>
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<pre style="margin: 0;"> <span id="LC701" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_complement_normalized</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">):</span></span>
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702
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<pre style="margin: 0;"> <span id="LC702" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span></span>
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703
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<pre style="margin: 0;"> <span id="LC703" class="line" lang="python"> <span class="s" style="color: #d14;">"--revcomp -g ^TTATTTGTCT -g ^TCCGCACTGG"</span><span class="p">,</span></span>
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704
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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python"> <span class="s" style="color: #d14;">"revcomp-single-normalize.fastq"</span><span class="p">,</span></span>
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705
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python"> <span class="s" style="color: #d14;">"revcomp.1.fastq"</span><span class="p">,</span></span>
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706
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_reverse_complement_and_info_file</span><span class="p">(</span><span class="n" style="color: #333;">run</span><span class="p">,</span> <span class="n" style="color: #333;">tmp_path</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="LC710" class="line" lang="python"> <span class="n" style="color: #333;">info_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"info.txt"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="python"> <span class="n" style="color: #333;">run</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="python"> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="python"> <span class="s" style="color: #d14;">"--revcomp"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"> <span class="s" style="color: #d14;">"-g"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python"> <span class="s" style="color: #d14;">"^TTATTTGTCT"</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;">"-g"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="python"> <span class="s" style="color: #d14;">"^TCCGCACTGG"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"> <span class="s" style="color: #d14;">"--info-file"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="python"> <span class="n" style="color: #333;">info_path</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"> <span class="s" style="color: #d14;">"revcomp-single-normalize.fastq"</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;">"revcomp.1.fastq"</span><span class="p">,</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC724" 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;">info_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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726
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<pre style="margin: 0;">+<span id="LC726" 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;">lines</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">6</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;">assert</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"read1/1"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">lines</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"read2/1 rc"</span></span>
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729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="731" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
731
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<pre style="margin: 0;">+<span id="LC731" 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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<td class="diff-line-num new new_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
732
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<pre style="margin: 0;">+<span id="LC732" 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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733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="python"></span>
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734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="python"></span>
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735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_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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736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmp_path</span> <span class="o" style="font-weight: 600;">/</span> <span class="s" style="color: #d14;">"input.fasta"</span></span>
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737
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<pre style="margin: 0;">+<span id="LC737" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_text</span><span class="p">(</span><span class="s" style="color: #d14;">">read</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">ACGTACGT</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--max-ee=0.001"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"/dev/null"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">)])</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#124a8b77d32c7ca9f7f1966a0cde3894ce860e05"><strong>tests/test_main.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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2
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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;">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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3
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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;">cutadapt.__main__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">main</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parse_cutoffs</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">parse_lengths</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CommandLineError</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">setup_logging</span></span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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5
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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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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_help</span><span class="p">():</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</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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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--help"</span><span class="p">])</span></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;">assert</span> <span class="n" style="color: #333;">e</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">args</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_cutoffs</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"5"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">5</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"6,7"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">7</span><span class="p">)</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"a,7"</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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"a"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"a,7"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="n" style="color: #333;">parse_cutoffs</span><span class="p">(</span><span class="s" style="color: #d14;">"1,2,3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_parse_lengths</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;">assert</span> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"25"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">,</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"17:25"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">17</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"25:"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="mi" style="color: #099;">25</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">":25"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">(</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="mi" style="color: #099;">25</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</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;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"1:2:3"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</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;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"a:2"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"a"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">parse_lengths</span><span class="p">(</span><span class="s" style="color: #d14;">"2:a"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="n" style="color: #333;">CommandLineError</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">parse_lengths</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="LC40" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_setup_logging</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">__name__</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">setup_logging</span><span class="p">(</span><span class="n" style="color: #333;">logger</span><span class="p">,</span> <span class="n" style="color: #333;">stdout</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;">quiet</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">minimal</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">debug</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Log message"</span><span class="p">)</span></span></pre>
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<li id="4ad7124461a591ee5c5c2e30f24380a477c3ed52">
<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#4ad7124461a591ee5c5c2e30f24380a477c3ed52"><strong>tests/test_paired.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">@@ -5,7 +5,7 @@ from itertools import product</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="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="LC8" 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 class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">redirect_stderr</span></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;">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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fixture</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">@@ -131,9 +131,8 @@ def test_no_trimming():</td>
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131
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_missing_file</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC135" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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136
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<pre style="margin: 0;">-<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span><span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_first_too_short</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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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,14 +143,13 @@ def test_first_too_short(tmpdir, cores):</td>
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144
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="python"> <span class="n" style="color: #333;">trunc1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</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;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="python"> <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>
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<pre style="margin: 0;">-<span id="LC151" class="line" lang="python"> <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC152" 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="LC153" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc1</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"/dev/null"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC150" 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="LC151" class="line" lang="python"> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc1</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.2.fastq"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="p">])</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>
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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;">test_second_too_short</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,14 +160,13 @@ def test_second_too_short(tmpdir, cores):</td>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lines</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">4</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"> <span class="n" style="color: #333;">trunc2</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">lines</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC165" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC166" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"> <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>
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="python"> <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">"--cores"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">cores</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python"> <span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"> <span class="n" style="color: #333;">main</span><span class="p">([</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"--paired-output"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"out.fastq"</span><span class="p">)),</span></span>
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<pre style="margin: 0;">+<span id="LC167" 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="LC168" class="line" lang="python"> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"paired.1.fastq"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">trunc2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_unmatched_read_names</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -327,10 +324,9 @@ def test_interleaved_neither_nor(tmpdir):</td>
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="n" style="color: #333;">p1</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"temp-paired.1.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">p2</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"temp-paired.2.fastq"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-a XX --interleaved"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p1"</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="s" style="color: #d14;">"paired.1.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="LC332" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="n" style="color: #333;">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="LC327" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="n" style="color: #333;">p1</span><span class="p">,</span> <span class="s" style="color: #d14;">"-p1"</span><span class="p">,</span> <span class="n" style="color: #333;">p2</span><span class="p">,</span> <span class="s" style="color: #d14;">"paired.1.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="LC328" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="python"> <span class="n" style="color: #333;">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="LC330" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_pair_filter_both</span><span class="p">(</span><span class="n" style="color: #333;">run_paired</span><span class="p">,</span> <span class="n" style="color: #333;">cores</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">@@ -504,25 +500,40 @@ def test_pair_adapters_demultiplexing(tmpdir):</td>
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<pre style="margin: 0;"> <span id="LC500" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_combinatorial_demultiplexing</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="LC503" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mark</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">parametrize</span><span class="p">(</span><span class="s" style="color: #d14;">"discarduntrimmed"</span><span class="p">,</span> <span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_combinatorial_demultiplexing</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">,</span> <span class="n" style="color: #333;">discarduntrimmed</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-g A=^AAAAAAAAAA -g C=^CCCCCCCCCC -G G=^GGGGGGGGGG -G T=^TTTTTTTTTT"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial.{name1}_{name2}.1.fasta"</span><span class="p">))]</span></span>
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510
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-p"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial.{name1}_{name2}.2.fasta"</span><span class="p">))]</span></span>
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511
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508
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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial.1.fasta"</span><span class="p">),</span> <span class="n" style="color: #333;">datapath</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial.2.fasta"</span><span class="p">)]</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="python"> <span class="n" style="color: #333;">combinations</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># third column says whether the file must exist</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"> <span class="p">]</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">discarduntrimmed</span><span class="p">:</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="python"> <span class="n" style="color: #333;">combinations</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"unknown"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">,</span> <span class="bp" style="color: #999;">False</span><span class="p">),</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="python"> <span class="p">]</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"> <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span><span class="s" style="color: #d14;">"--discard-untrimmed"</span><span class="p">]</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="python"> <span class="n" style="color: #333;">combinations</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">[</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"unknown"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">),</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="python"> <span class="p">]</span></span>
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512
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">main</span><span class="p">(</span><span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC516" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC517" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC518" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"unknown"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"unknown"</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC520" class="line" lang="python"> <span class="p">]:</span></span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="p">,</span> <span class="n" style="color: #333;">should_exist</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">combinations</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC529" 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;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"combinatorial.{name1}_{name2}.{i}.fasta"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">name1</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name1</span><span class="p">,</span> <span class="n" style="color: #333;">name2</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">name2</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutpath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"combinatorial"</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Output file missing"</span></span>
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<pre style="margin: 0;">-<span id="LC525" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)))</span></span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">should_exist</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Output file missing"</span></span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="python"> <span class="n" style="color: #333;">assert_files_equal</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)))</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">tmpdir</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check</span><span class="p">(),</span> <span class="s" style="color: #d14;">"Output file should not exist"</span></span>
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537
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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC538" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_info_file</span><span class="p">(</span><span class="n" style="color: #333;">tmpdir</span><span class="p">):</span></span>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#9627b71ff9952493fda5865aea912319edd1cdd2"><strong>tests/test_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">@@ -4,6 +4,7 @@ import pytest</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;">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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5
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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;">cutadapt.adapters</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Where</span><span class="p">,</span> <span class="n" style="color: #333;">WhereToRemove</span><span class="p">,</span> <span class="n" style="color: #333;">LinkedAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">SingleAdapter</span></span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.parser</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterParser</span><span class="p">,</span> <span class="n" style="color: #333;">AdapterSpecification</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ModificationInfo</span></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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8
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_expand_braces</span><span class="p">():</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -178,5 +179,5 @@ def test_anywhere_parameter():</td>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"> <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'foo1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGAAGTACACGGTTAAAAAAAAAA'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterCutter</span></span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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182
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">''</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#a29298d28cfcb546445a18cc3462646626165ac4"><strong>tests/test_qualtrim.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;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnaio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Sequence</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cutadapt.qualtrim</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">nextseq_trim_index</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.qualtrim</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">nextseq_trim_index</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">expected_errors</span></span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_nextseq_trim</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">@@ -11,3 +13,22 @@ def test_nextseq_trim():</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">'AA//EAEE//A6///E//A//EA/EEEEEEAEA//EEEEEEEEEEEEEEE###########EE#EA'</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">nextseq_trim_index</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">22</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">33</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_expected_errors</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">encode_qualities</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">""</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">chr</span><span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">33</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">quals</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</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="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.01</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">20</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;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.001</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">30</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.11</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">10</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 class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.3</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</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;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.111</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">pytest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">approx</span><span class="p">(</span><span class="mf" style="color: #099;">0.2111</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_errors</span><span class="p">(</span><span class="n" style="color: #333;">encode_qualities</span><span class="p">([</span><span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">]))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#bb92bf4985f91906d71414ff1f007cc598adff83"><strong>tests/test_trim.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;">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="LC2" 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;">SingleAdapter</span><span class="p">,</span> <span class="n" style="color: #333;">Where</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;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterCutter</span></span>
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<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;">cutadapt.modifiers</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">ModificationInfo</span></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>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_statistics</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;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'name'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AAAACCCCAAAA'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"> <span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">SingleAdapter</span><span class="p">(</span><span class="s" style="color: #d14;">'CCCC'</span><span class="p">,</span> <span class="n" style="color: #333;">Where</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">BACK</span><span class="p">,</span> <span class="n" style="color: #333;">max_error_rate</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</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;">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="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TODO make this a lot simpler</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_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="LC13" 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="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">@@ -29,7 +29,7 @@ def test_end_trim_with_mismatch():</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'foo1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AAAAAAAAAAATCGTCGATC'</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;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">],</span> <span 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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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'AAAAAAAAAAA'</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">cutter</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;">adapter</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lengths</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">{</span><span class="mi" style="color: #099;">9</span><span class="p">:</span> <span class="mi" style="color: #099;">1</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">@@ -39,7 +39,7 @@ def test_end_trim_with_mismatch():</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'foo2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'AAAAAAAAAAATCGAACGA'</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;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">],</span> <span 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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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">cutter</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;">adapter</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">back</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lengths</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">@@ -57,5 +57,5 @@ def test_anywhere_with_errors():</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <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;">read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Sequence</span><span class="p">(</span><span class="s" style="color: #d14;">'foo'</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="LC59" class="line" lang="python"> <span class="n" style="color: #333;">cutter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">AdapterCutter</span><span class="p">([</span><span class="n" style="color: #333;">adapter</span><span class="p">],</span> <span 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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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="p"><span class="idiff left right">[]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">trimmed_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cutter</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ModificationInfo</span></span><span class="p"><span class="idiff right">()</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">trimmed_read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_trimmed</span></span></pre>
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<a href="https://salsa.debian.org/med-team/python-cutadapt/-/commit/afc23835c3b1b22776876ed5f9011295b0059b30#570726290219a04b926b9aa2c02fe1ba4204124a"><strong>tests/utils.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">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;">from</span> <span class="nn" style="color: #555;">contextlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">contextmanager</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">contextmanager</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">redirect_stderr</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"> <span class="s" style="color: #d14;">"""Send stderr to stdout. Nose doesn't capture stderr, yet."""</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">old_stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stdout</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">old_stderr</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">datapath</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">):</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,6 +8,7 @@ deps =</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest-timeout</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">pytest-mock</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="ini"><span class="py">setenv</span> <span class="p">=</span> <span class="s" style="color: #d14;">PYTHONDEVMODE = 1</span></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span></span>
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13
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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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13
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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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,10 +32,6 @@ basepython = python3.6</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="ini"><span class="py">deps</span> <span class="p">=</span> <span class="s" style="color: #d14;">mypy</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="ini"><span class="py">commands</span> <span class="p">=</span> <span class="s" style="color: #d14;">mypy src/</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="ini"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="ini"><span class="nn" style="color: #555;">[travis]</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="ini"><span class="py">python</span> <span class="p">=</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="ini"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">3.6:</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">py36,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">docs,</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">mypy</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="ini"><span class="nn" style="color: #555;">[coverage:run]</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="ini"><span class="py">parallel</span> <span class="p">=</span> <span class="s" style="color: #d14;">True</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="ini"><span class="py">include</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">@@ -48,6 +45,6 @@ source =</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="ini"></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="ini"><span class="nn" style="color: #555;">[flake8]</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="ini"><span class="py">max-line-length</span> <span class="p">=</span> <span class="s" style="color: #d14;">120</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="ini"><span class="py">max-complexity</span> <span class="p">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">20</span></span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="ini"><span class="py">max-complexity</span> <span class="p">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">16</span></span></span>
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52
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="ini"><span class="py">select</span> <span class="p">=</span> <span class="s" style="color: #d14;">E,F,W,C90,W504</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="ini"><span class="py">extend_ignore</span> <span class="p">=</span> <span class="s" style="color: #d14;">E128,E131,W503,E203</span></span></pre>
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