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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/q2-quality-filter">Debian Med / q2-quality-filter</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329">5e6c8680</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-12-03T13:58:37+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2020.11.0</pre>
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<h4>13 changed files:</h4>
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#5aa1b4f51558ea2abc03e6ee64608c625f71d973">
q2_quality_filter/__init__.py
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<li class="file-stats">
<a href="#25308bea9452c7b9fdf0f946c87702b0e5915866">
q2_quality_filter/_filter.py
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<li class="file-stats">
<a href="#3092241a8423da6faa6cce3a181862e5852e4e37">
q2_quality_filter/_format.py
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<li class="file-stats">
<a href="#743e812b6a006c043f204cda457dba7fac912362">
q2_quality_filter/_transformer.py
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<li class="file-stats">
<a href="#82fee5e4f5aa9ba1f6072cd26184c21e18baffd9">
q2_quality_filter/_type.py
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<li class="file-stats">
<a href="#98ca41a00ca803667e6d5ab74cd3d614cb003e35">
q2_quality_filter/_version.py
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<li class="file-stats">
<a href="#c4adc5a8b3616a1d6a4e31cf016c589f15ef9f50">
q2_quality_filter/plugin_setup.py
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<li class="file-stats">
<a href="#35068546a38046c533777d03e1ab29a215b0936d">
q2_quality_filter/test/__init__.py
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<li class="file-stats">
<a href="#e0920c763105e13fb9a21af340562a94fef61ef7">
q2_quality_filter/test/test_filter.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,7 +14,7 @@ install:</td>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml</span></span>
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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda env create -q -n test-env --file qiime2-latest-py36-linux-conda.yml</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">source activate test-env</span></span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q <span class="idiff left right">nose</span></span></span>
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<td class="diff-line-num new old_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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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q <span class="idiff left right">pytest-cov</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q flake8</span></span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -q https://github.com/qiime2/q2lint/archive/master.zip</span></span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make install</span></span>
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<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">
<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">BSD 3-Clause License</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">Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">All rights reserved.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,10 +9,10 @@ lint:</td>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="make"> flake8</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="make"> <span class="idiff left right">nosetests</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="make"> <span class="idiff left right">py.test</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nl">test-cov</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"> <span class="idiff left right">nosetests</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"> <span class="idiff left">py.test </span><span class="nt" style="color: #000080;"><span class="idiff">--cov</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">q2_quality_filter</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">all</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"> <span class="nv" style="color: #008080;">$(PYTHON)</span> setup.py <span class="nb" style="color: #0086b3;">install</span></span>
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<li id="5aa1b4f51558ea2abc03e6ee64608c625f71d973">
<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#5aa1b4f51558ea2abc03e6ee64608c625f71d973"><strong>q2_quality_filter/__init__.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</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;"># The full license is in the file LICENSE, distributed with this software.</span></span>
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<pre style="margin: 0;"> <span id="LC7" 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="LC8" class="line" lang="python"></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;">._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">q_score</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">q_score_joined</span></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;">._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">q_score</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;">._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_versions</span></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="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_versions</span><span class="p">()[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">del</span> <span class="n" style="color: #333;">get_versions</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'q_score_joined'</span></span><span class="p">]</span></span></pre>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">]</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#25308bea9452c7b9fdf0f946c87702b0e5915866"><strong>q2_quality_filter/_filter.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</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">@@ -61,6 +61,7 @@ _default_params = {</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="p">}</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>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># TODO: fix up demux fmt writing a la q2-cutadapt</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">demux</span><span class="p">:</span> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">min_quality</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'min_quality'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">quality_window</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'quality_window'</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">@@ -182,16 +183,3 @@ def q_score(demux: SingleLanePerSampleSingleEndFastqDirFmt,</td>
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<pre style="margin: 0;"> <span id="LC183" 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;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">).</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">result</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span></span></pre>
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">q_score_joined</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"> <span class="n" style="color: #333;">demux</span><span class="p">:</span> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"> <span class="n" style="color: #333;">min_quality</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'min_quality'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">quality_window</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'quality_window'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"> <span class="n" style="color: #333;">min_length_fraction</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="nb" style="color: #0086b3;">float</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'min_length_fraction'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"> <span class="n" style="color: #333;">max_ambiguous</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_default_params</span><span class="p">[</span><span class="s" style="color: #d14;">'max_ambiguous'</span><span class="p">])</span> \</span>
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"> <span class="o" style="font-weight: 600;">-></span> <span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">demux</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="p">,</span> <span class="n" style="color: #333;">quality_window</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"> <span class="n" style="color: #333;">min_length_fraction</span><span class="p">,</span> <span class="n" style="color: #333;">max_ambiguous</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#3092241a8423da6faa6cce3a181862e5852e4e37"><strong>q2_quality_filter/_format.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</span></span>
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<pre style="margin: 0;"> <span id="LC1" 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="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#82fee5e4f5aa9ba1f6072cd26184c21e18baffd9"><strong>q2_quality_filter/_type.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#98ca41a00ca803667e6d5ab74cd3d614cb003e35"><strong>q2_quality_filter/_version.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">@@ -23,9 +23,9 @@ def get_keywords():</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">tag: 2019.10</span>.0)"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">fb46c1bd105da7b65d4294351bb1b1cb48f10e48</span>"</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"20<span class="idiff left right">19-11-01 01:04:25</span> +0000"</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (<span class="idiff left right">HEAD -> master, tag: 2020.11</span>.0)"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">bdafd7e885b351a99dc45a54abf5fdc1990823b6</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">git_date</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"20<span class="idiff left right">20-11-25 17:13:08</span> +0000"</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">,</span> <span class="s" style="color: #d14;">"date"</span><span class="p">:</span> <span class="n" style="color: #333;">git_date</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;">return</span> <span class="n" style="color: #333;">keywords</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#c4adc5a8b3616a1d6a4e31cf016c589f15ef9f50"><strong>q2_quality_filter/plugin_setup.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</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 +41,14 @@ plugin.register_semantic_type_to_format(</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">QualityFilterStats</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;">artifact_format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">QualityFilterStatsDirFmt</span><span class="p">)</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="n" style="color: #333;">InputMap</span><span class="p">,</span> <span class="n" style="color: #333;">OutputMap</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">TypeMap</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;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">SequencesWithQuality</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">PairedEndSequencesWithQuality</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;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">SequencesWithQuality</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="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">JoinedSequencesWithQuality</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;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">JoinedSequencesWithQuality</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="p">})</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">_q_score_parameters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="s" style="color: #d14;">'min_quality'</span><span class="p">:</span> <span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">Int</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="s" style="color: #d14;">'quality_window'</span><span class="p">:</span> <span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">Int</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">@@ -76,11 +84,10 @@ _q_score_output_descriptions = {</td>
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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="LC85" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">.</span><span class="n" style="color: #333;">register_function</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q2_quality_filter</span><span class="p">.</span><span class="n" style="color: #333;">q_score</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'demux'</span><span class="p">:</span> <span class="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">SequencesWithQuality</span> <span class="o" style="font-weight: 600;">|</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">PairedEndSequencesWithQuality</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'demux'</span><span class="p">:</span> <span class="n" style="color: #333;">InputMap</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_parameters</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filtered_sequences'</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">SampleData</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">SequencesWithQuality</span></span><span class="p"><span class="idiff right">]</span>),</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filtered_sequences'</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">OutputMap</span></span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filter_stats'</span><span class="p">,</span> <span class="n" style="color: #333;">QualityFilterStats</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">input_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_input_descriptions</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">@@ -91,20 +98,4 @@ plugin.methods.register_function(</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="s" style="color: #d14;">'the presence of ambiguous base calls.'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">.</span><span class="n" style="color: #333;">register_function</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">function</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">q2_quality_filter</span><span class="p">.</span><span class="n" style="color: #333;">q_score_joined</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">inputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'demux'</span><span class="p">:</span> <span class="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">JoinedSequencesWithQuality</span><span class="p">]},</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">parameters</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_parameters</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">outputs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filtered_sequences'</span><span class="p">,</span> <span class="n" style="color: #333;">SampleData</span><span class="p">[</span><span class="n" style="color: #333;">JoinedSequencesWithQuality</span><span class="p">]),</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'filter_stats'</span><span class="p">,</span> <span class="n" style="color: #333;">QualityFilterStats</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">input_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_input_descriptions</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">parameter_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_parameter_descriptions</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">output_descriptions</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">_q_score_output_descriptions</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC105" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Quality filter based on joined sequence quality scores.'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'This method filters joined sequence based on quality '</span></span>
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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python"> <span class="s" style="color: #d14;">'scores and the presence of ambiguous base calls.'</span></span>
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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"><span class="n" style="color: #333;">importlib</span><span class="p">.</span><span class="n" style="color: #333;">import_module</span><span class="p">(</span><span class="s" style="color: #d14;">'q2_quality_filter._transformer'</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#35068546a38046c533777d03e1ab29a215b0936d"><strong>q2_quality_filter/test/__init__.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#e0920c763105e13fb9a21af340562a94fef61ef7"><strong>q2_quality_filter/test/test_filter.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2016-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2016-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</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;">#</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 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">gzip</span></span>
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<pre style="margin: 0;">+<span id="LC11" 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="LC12" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas.util.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</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">@@ -16,12 +17,17 @@ from qiime2.sdk import Artifact</td>
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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;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">npt</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;">qiime2.plugin.testing</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">TestPluginBase</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;">qiime2.util</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">redirected_stdio</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;">q2_types.per_sample_sequences</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">FastqGzFormat</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_quality_filter._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span><span class="n" style="color: #333;">_read_fastq_seqs</span><span class="p">,</span> <span class="n" style="color: #333;">_runs_of_ones</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;">_truncate</span><span class="p">,</span> <span class="n" style="color: #333;">q_score</span><span class="p">,</span> <span class="n" style="color: #333;">q_score_joined</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;">FastqGzFormat</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;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="p">)</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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_quality_filter._filter</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">_read_fastq_seqs</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">_runs_of_ones</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">_truncate</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">q2_quality_filter._format</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">QualityFilterStatsFmt</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,16 +81,20 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_q_score_all_dropped</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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77
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Artifact</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'simple.qza'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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79
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84
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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="LC85" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertRaisesRegex</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ValueError</span><span class="p">,</span> <span class="s" style="color: #d14;">"filtered out"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">):</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span><span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">50</span><span class="p">)</span></span>
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82
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88
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_q_score_numeric_ids</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Artifact</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'numeric_ids.qza'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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86
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">exp_sids</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'00123'</span><span class="p">,</span> <span class="s" style="color: #d14;">'0.4560'</span><span class="p">}</span></span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">obs_ar</span><span class="p">,</span> <span class="n" style="color: #333;">stats_ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC97" 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;">stats_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">obs_manifest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">manifest</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">manifest</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">obs_manifest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">read_csv</span><span class="p">(</span><span class="n" style="color: #333;">obs_manifest</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(),</span> <span class="n" style="color: #333;">dtype</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;">comment</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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100
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">obs_manifest</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</span><span class="p">,</span> <span class="n" style="color: #333;">inplace</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,10 +105,12 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_q_score</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="LC107" class="line" lang="python"> <span class="n" style="color: #333;">ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Artifact</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'simple.qza'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">obs_drop_ambig</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">quality_window</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.25</span><span class="p">)</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">):</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">obs_drop_ambig_ar</span><span class="p">,</span> <span class="n" style="color: #333;">stats_ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">quality_window</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;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.25</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">obs_drop_ambig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_drop_ambig_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="python"> <span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">stats_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</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="n" style="color: #333;">exp_drop_ambig</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"@foo_1"</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python"> <span class="s" style="color: #d14;">"ATGCATGC"</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">@@ -108,19 +120,23 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-truncated'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-too-short-after-truncation'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-exceeding-maximum-ambiguous-bases'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">exp_drop_ambig_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </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="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">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</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">0</span></span><span class="p"><span class="idiff">,</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 right">1</span></span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python"> <span class="n" style="color: #333;">exp_drop_ambig_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mf" style="color: #099;">2<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" 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="LC124" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" 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="LC125" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">exp_drop_ambig_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp_drop_ambig_stats</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_drop_ambig</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">.</span><span class="n" style="color: #333;">iter_views</span><span class="p">(</span><span class="n" style="color: #333;">FastqGzFormat</span><span class="p">)</span></span>
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117
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iterator</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_drop_ambig</span><span class="p">)</span></span>
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132
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">exp_drop_ambig_stats</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC122" class="line" lang="python"> <span class="n" style="color: #333;">obs_trunc</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">quality_window</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</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="LC123" class="line" lang="python"> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.25</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;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</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;">obs_trunc_ar</span><span class="p">,</span> <span class="n" style="color: #333;">stats_ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="python"> <span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">quality_window</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.25</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="python"> <span class="n" style="color: #333;">obs_trunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_trunc_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC138" 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;">stats_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="n" style="color: #333;">exp_trunc</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"@foo_1"</span><span class="p">,</span></span>
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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="s" style="color: #d14;">"ATGCATGC"</span><span class="p">,</span></span>
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142
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"> <span class="s" style="color: #d14;">"+"</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">@@ -129,22 +145,24 @@ class FilterTests(TestPluginBase):</td>
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145
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="s" style="color: #d14;">"ATA"</span><span class="p">,</span></span>
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146
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="s" style="color: #d14;">"+"</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"> <span class="s" style="color: #d14;">"DDD"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"> <span class="n" style="color: #333;">exp_trunc_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </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="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">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">),</span></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </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="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</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 right">0</span></span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">exp_trunc_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mf" style="color: #099;">2<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">1.</span></span><span class="p">),</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'bar'</span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">1.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">0.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.</span></span><span class="p">)],</span></span>
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134
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150
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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135
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151
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">exp_trunc_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp_trunc_stats</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</span><span class="p">)</span></span>
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136
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152
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python"></span>
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137
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153
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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138
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154
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">obs_trunc</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">.</span><span class="n" style="color: #333;">iter_views</span><span class="p">(</span><span class="n" style="color: #333;">FastqGzFormat</span><span class="p">):</span></span>
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139
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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140
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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
156
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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="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">exp_trunc</span><span class="p">))</span></span>
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141
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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;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">exp_trunc_stats</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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142
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"></span>
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143
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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
159
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_q_score_real</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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144
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Artifact</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'real_data.qza'</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="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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146
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">obs_result</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_score</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">40</span><span class="p">,</span></span>
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147
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.24</span><span class="p">)</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">):</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python"> <span class="n" style="color: #333;">obs_ar</span><span class="p">,</span> <span class="n" style="color: #333;">stats_ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span></span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="python"> <span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.24</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;">obs_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC165" 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;">stats_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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148
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># All input reads are represented here in their post-quality filtered</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># form. Reads that are commented out were manually identified as being</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -213,21 +231,23 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-truncated'</span><span class="p">,</span></span>
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-too-short-after-truncation'</span><span class="p">,</span></span>
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233
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-exceeding-maximum-ambiguous-bases'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">10</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mf" style="color: #099;">10<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">6.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">10.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">4.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.</span></span><span class="p">)],</span></span>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp_stats</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</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;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_result</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">.</span><span class="n" style="color: #333;">iter_views</span><span class="p">(</span><span class="n" style="color: #333;">FastqGzFormat</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iterator</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_result</span><span class="p">)</span></span>
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">exp_stats</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_q_score_real_joined</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="LC245" class="line" lang="python"> <span class="n" style="color: #333;">ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Artifact</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">get_data_path</span><span class="p">(</span><span class="s" style="color: #d14;">'real_data_joined.qza'</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"> <span class="n" style="color: #333;">obs_result</span><span class="p">,</span> <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">q_score_joined</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.24</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">redirected_stdio</span><span class="p">(</span><span class="n" style="color: #333;">stdout</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">devnull</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">obs_ar</span><span class="p">,</span> <span class="n" style="color: #333;">stats_ar</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">plugin</span><span class="p">.</span><span class="n" style="color: #333;">methods</span><span class="p">[</span><span class="s" style="color: #d14;">'q_score'</span><span class="p">](</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">ar</span><span class="p">,</span> <span class="n" style="color: #333;">min_quality</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="n" style="color: #333;">min_length_fraction</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.24</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;">obs_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">SingleLanePerSampleSingleEndFastqDirFmt</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;">stats_ar</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># All input reads are represented here in their post-quality filtered</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># form. Reads that are commented out were manually identified as being</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">@@ -296,13 +316,13 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-truncated'</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="s" style="color: #d14;">'reads-too-short-after-truncation'</span><span class="p">,</span></span>
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-exceeding-maximum-ambiguous-bases'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">6</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">10</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">4</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">)],</span></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">([(</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="mf" style="color: #099;">10<span class="idiff left">.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">6.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">10.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">4.</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.</span></span><span class="p">)],</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">columns</span><span class="p">)</span></span>
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">exp_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">exp_stats</span><span class="p">.</span><span class="n" style="color: #333;">set_index</span><span class="p">(</span><span class="s" style="color: #d14;">'sample-id'</span><span class="p">)</span></span>
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302
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python"> <span class="n" style="color: #333;">iterator</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">obs_result</span><span class="p">.</span><span class="n" style="color: #333;">sequences</span><span class="p">.</span><span class="n" style="color: #333;">iter_views</span><span class="p">(</span><span class="n" style="color: #333;">FastqGzFormat</span><span class="p">)</span></span>
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304
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324
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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sample_id</span><span class="p">,</span> <span class="n" style="color: #333;">fp</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iterator</span><span class="p">:</span></span>
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305
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<pre style="margin: 0;">-<span id="LC305" class="line" lang="python"> <span class="n" style="color: #333;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">l</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">l</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</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;">obs</span><span class="p">.</span><span class="n" style="color: #333;">extend</span><span class="p">([</span><span class="n" style="color: #333;"><span class="idiff left">x</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">strip</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">x</span></span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">gzip</span><span class="p">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">),</span> <span class="s" style="color: #d14;">'rt'</span><span class="p">)])</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">,</span> <span class="n" style="color: #333;">exp_result</span><span class="p">)</span></span>
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327
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<pre style="margin: 0;"> <span id="LC327" class="line" lang="python"> <span class="n" style="color: #333;">pdt</span><span class="p">.</span><span class="n" style="color: #333;">assert_frame_equal</span><span class="p">(</span><span class="n" style="color: #333;">stats</span><span class="p">,</span> <span class="n" style="color: #333;">exp_stats</span><span class="p">.</span><span class="n" style="color: #333;">loc</span><span class="p">[</span><span class="n" style="color: #333;">stats</span><span class="p">.</span><span class="n" style="color: #333;">index</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/5e6c8680848f5f036216d8a2bbe8de33f318d329#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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;"># ----------------------------------------------------------------------------</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;"># Copyright (c) 2017-20<span class="idiff left right">19</span>, QIIME 2 development team.</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;"># Copyright (c) 2017-20<span class="idiff left right">20</span>, QIIME 2 development team.</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;">#</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;"># Distributed under the terms of the Modified BSD License.</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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