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<h3>
Andreas Tille pushed to branch master
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/67aab201bcef1ab6d86fefe5d8ad46741e60f59d">67aab201</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:54:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2021.8.0</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/df2c8aafcc0d00d5d624f26a1d994ad8721e9670">df2c8aaf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:54:42+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/f26726a80bb3ea4abee286c4205daed773ef3432">f26726a8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:54:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2021.8.0'
Update to upstream version '2021.8.0'
with Debian dir c725977e3c372ab978d7d4bd54cdc9538d682289</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/d9485c53fa09a5332d82d280f5709d5774df61bf">d9485c53</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:54:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Standards-Version: 4.6.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/f3f5c2db9ed1d58c25062b0bcbb43fafc3faa7f7">f3f5c2db</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:56:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Versioned (Build-)Depends on qiime and q2 modules (>= 2021.8.0)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/q2-quality-filter/-/commit/1d63a906cddfe182f42f6fb39aace3d9397f8a90">1d63a906</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-09-29T16:58:19+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>18 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#899ce9c202bf7bb5480e72836c3edc773c9c4244">
<span class="new-file">
+
.github/workflows/ci.yml
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
<span class="deleted-file">
−
.travis.yml
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<li class="file-stats">
<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">
LICENSE
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#243f1ef343e8375e9296d24d5fc49b37a3869bcc">
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−
ci/recipe/conda_build_config.yaml
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<li class="file-stats">
<a href="#22fbe0b68848772d4b1c45f0d62dcd71a06cde00">
ci/recipe/meta.yaml
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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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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</ul>
<h4>Changes:</h4>
<li id="899ce9c202bf7bb5480e72836c3edc773c9c4244">
<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#899ce9c202bf7bb5480e72836c3edc773c9c4244"><strong>.github/workflows/ci.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># This file is automatically generated by busywork.qiime2.org and</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># template-repos - any manual edits made to this file will be erased when</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># busywork performs maintenance updates.</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">ci</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">pull_request</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">lint</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">checkout source</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">set up python </span><span class="m" style="color: #099;">3.8</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v1</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="m" style="color: #099;">3.8</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">install dependencies</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">python -m pip install --upgrade pip</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">lint</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install -q https://github.com/qiime2/q2lint/archive/master.zip</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="s" style="color: #d14;">q2lint</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install -q flake8</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">flake8</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-and-test</span><span class="pi">:</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">needs</span><span class="pi">:</span> <span class="s" style="color: #d14;">lint</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-latest</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-latest</span><span class="pi">]</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">checkout source</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">fetch-depth</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">set up git repo for versioneer</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="s" style="color: #d14;">git fetch --depth=1 origin +refs/tags/*:refs/tags/*</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">qiime2/action-library-packaging@alpha1</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">package-name</span><span class="pi">:</span> <span class="s" style="color: #d14;">q2-quality-filter</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">build-target</span><span class="pi">:</span> <span class="s" style="color: #d14;">dev</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">additional-tests</span><span class="pi">:</span> <span class="s" style="color: #d14;">py.test --pyargs q2_quality_filter</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">library-token</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ secrets.LIBRARY_TOKEN }}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export MPLBACKEND='Agg'</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">wget -q https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export MINICONDA_PREFIX="$HOME/miniconda"</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash miniconda.sh -b -p $MINICONDA_PREFIX</span></span>
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9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export PATH="$MINICONDA_PREFIX/bin:$PATH"</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda config --set always_yes yes</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda update -q conda</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda info -a</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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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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<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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<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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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">conda install -q pytest-cov</span></span>
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18
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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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19
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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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20
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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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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make lint</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make test-cov</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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="LC3" class="line" lang="plaintext">Copyright (c) 2017-202<span class="idiff left right">0</span>, QIIME 2 development team.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Copyright (c) 2017-202<span class="idiff left right">1</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="LC6" class="line" lang="plaintext">Redistribution and use in source and binary forms, with or without</span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># q2-quality-filter</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p"><span class="idiff left">[</span></span><span class="nv" style="color: #008080;">![<span class="idiff">Build Status</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://travis-ci.org/qiime2/q2-quality-filter.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org/qiime2/q2-quality-filter</span>)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown">This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.</span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#243f1ef343e8375e9296d24d5fc49b37a3869bcc"><strong>ci/recipe/conda_build_config.yaml</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"> <span class="pi">-</span> <span class="m" style="color: #099;">3.6</span></span></pre>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#22fbe0b68848772d4b1c45f0d62dcd71a06cde00"><strong>ci/recipe/meta.yaml</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set data = load_setup_py_data() %</span><span class="pi">}</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set version = data.get('version') or 'placehold' %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="pi">{</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span> <span class="nv" style="color: #008080;">set release = '.'.join(version.split('.')</span><span class="pi">[:</span><span class="nv" style="color: #008080;">2</span><span class="pi">]</span><span class="nv" style="color: #008080;">) %</span><span class="pi">}</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">q2-quality-filter</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,11 +19,18 @@ requirements:</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python {{ python }}</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pandas</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 {{ release }}.*</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates {{ release }}.*</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types {{ release }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">numpy</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 {{ qiime2_epoch }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates {{ qiime2_epoch }}.*</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types {{ qiime2_epoch }}.*</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">requires</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2 >={{ qiime2 }}</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2templates >={{ q2templates }}</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2-types >={{ q2_types }}</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pytest</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">imports</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">q2_quality_filter</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">qiime2.plugins.quality_filter</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">q2-quality-filter (202<span class="idiff left right">0.11.1-3) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">q2-quality-filter (202<span class="idiff left right">1.8.0-1) unstable</span>; urgency=medium</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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> [ Étienne Mollier ]</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * d/control: update uploader address</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * d/watch: fix broken url to github</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> * d/salsa-ci.yml: disable test on i386; python3-skbio missing on i386</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org> Mon, 05 Jul 2021 22:39:37 +0200</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Standards-Version: 4.6.0 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> * Versioned (Build-)Depends on qiime and q2 modules (>= 2021.8.0)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 29 Sep 2021 16:56:59 +0200</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">q2-quality-filter (2020.11.1-2) unstable; urgency=medium</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">@@ -9,10 +9,10 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">setuptools</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">nose</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">20<span class="idiff left right">19.10</span>.0</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">5.1</span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span> <span class="p">(>=</span> <span class="m" style="color: #099;">20<span class="idiff left right">21.8</span>.0</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"><span class="n" style="color: #333;">Standards</span><span class="p">-</span><span class="k" style="font-weight: 600;">Version</span><span class="p">:</span> <span class="m" style="color: #099;">4.<span class="idiff left right">6.0</span></span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Browser</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">quality</span><span class="p">-</span><span class="n" style="color: #333;">filter</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="mosel"><span class="n" style="color: #333;">Vcs</span><span class="p">-</span><span class="n" style="color: #333;">Git</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">salsa</span><span class="p">.</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">/</span><span class="n" style="color: #333;">med</span><span class="p">-</span><span class="n" style="color: #333;">team</span><span class="p">/</span><span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">quality</span><span class="p">-</span><span class="n" style="color: #333;">filter</span><span class="p">.</span><span class="n" style="color: #333;">git</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">https</span><span class="p">://</span><span class="n" style="color: #333;">qiime2</span><span class="p">.</span><span class="n" style="color: #333;">org</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">@@ -24,9 +24,9 @@ Depends: ${shlibs:Depends},</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">misc</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="mosel"> <span class="p">${</span><span class="n" style="color: #333;">python3</span><span class="p">:</span><span class="n" style="color: #333;">Depends</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">python3</span><span class="p">-</span><span class="n" style="color: #333;">pandas</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> <span class="n" style="color: #333;">qiime</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="n" style="color: #333;">q2templates</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span>,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"> <span class="n" style="color: #333;">q2</span><span class="p">-</span><span class="n" style="color: #333;">types</span><span class="idiff left"> </span><span class="p"><span class="idiff">(>=</span></span><span class="idiff"> </span><span class="m" style="color: #099;"><span class="idiff">2021.8.0</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="mosel"><span class="n" style="color: #333;">Description</span><span class="p">:</span> <span class="n" style="color: #333;">QIIME2</span> <span class="n" style="color: #333;">plugin</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">PHRED</span><span class="p">-</span><span class="n" style="color: #333;">based</span> <span class="n" style="color: #333;">filtering</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">trimming</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="mosel"> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">powerful</span><span class="p">,</span> <span class="n" style="color: #333;">extensible</span><span class="p">,</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">decentralized</span> <span class="n" style="color: #333;">microbiome</span> <span class="n" style="color: #333;">analysis</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">focus</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">data</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">analysis</span> <span class="n" style="color: #333;">transparency</span><span class="p">.</span> <span class="n" style="color: #333;">QIIME</span> <span class="m" style="color: #099;">2</span> <span class="n" style="color: #333;">enables</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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">@@ -20,10 +20,11 @@ from q2_types.per_sample_sequences import (</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_fastq_seqs</span><span class="p">(</span><span class="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="n" style="color: #333;">phred_offset</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># This function is adapted from @jairideout's SO post:</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># http://stackoverflow.com/a/39302117/3424666</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">fh</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">t</span>'</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;">fh</span> <span class="o" style="font-weight: 600;">=</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="n" style="color: #333;">filepath</span><span class="p">,</span> <span class="s" style="color: #d14;">'r<span class="idiff left right">b</span>'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq_header</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual_header</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">itertools</span><span class="p">.</span><span class="n" style="color: #333;">zip_longest</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="p">[</span><span class="n" style="color: #333;">fh</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">()</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">qual_parsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">fromstring</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint8</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">phred_offset</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">qual_parsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">frombuffer</span><span class="p">(</span><span class="nb" style="color: #0086b3;">memoryview</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">),</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">uint8</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;">qual_parsed</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">qual_parsed</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">phred_offset</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="p">(</span><span class="n" style="color: #333;">seq_header</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),</span> <span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),</span> <span class="n" style="color: #333;">qual_header</span><span class="p">.</span><span class="n" style="color: #333;">strip</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;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">qual_parsed</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,7 +87,8 @@ def q_score(demux: SingleLanePerSampleSingleEndFastqDirFmt,</td>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"> <span class="n" style="color: #333;">log_records_totalkept_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">metadata_view</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demux</span><span class="p">.</span><span class="n" style="color: #333;">metadata</span><span class="p">.</span><span class="n" style="color: #333;">view</span><span class="p">(</span><span class="n" style="color: #333;">YamlFormat</span><span class="p">).</span><span class="nb" style="color: #0086b3;">open</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;">phred_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yaml</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">metadata_view</span><span class="p">)[</span><span class="s" style="color: #d14;">'phred-offset'</span><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">phred_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">yaml</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">metadata_view</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">Loader</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">yaml</span><span class="p">.</span><span class="n" style="color: #333;">SafeLoader</span><span class="p">)[</span><span class="s" style="color: #d14;">'phred-offset'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">demux_manifest</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">demux</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;">demux</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="LC93" class="line" lang="python"> <span class="n" style="color: #333;">demux_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;">demux_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>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">demux_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;">'filename'</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="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,12 +141,11 @@ def q_score(demux: SingleLanePerSampleSingleEndFastqDirFmt,</td>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># do not keep the read if there are too many ambiguous bases</span></span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_ambiguous</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_record</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">].</span><span class="n" style="color: #333;">count</span><span class="p">(</span><span class="sa"><span class="idiff left right">b</span></span><span class="s" style="color: #d14;">'N'</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_ambiguous</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python"> <span class="n" style="color: #333;">log_records_max_ambig_counts</span><span class="p">[</span><span class="n" style="color: #333;">sample_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"> <span class="n" style="color: #333;">fastq_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sequence_record</span><span class="p">[:</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"> <span class="n" style="color: #333;">fastq_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fastq_lines</span><span class="p">.</span><span class="n" style="color: #333;">encode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</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;">fastq_lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">sequence_record</span><span class="p">[:</span><span class="mi" style="color: #099;">4</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="sa">b</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">writer</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python"> <span class="n" style="color: #333;">writer</span> <span class="o" style="font-weight: 600;">=</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;">path</span><span class="p">),</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'w'</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#743e812b6a006c043f204cda457dba7fac912362"><strong>q2_quality_filter/_transformer.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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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">@@ -7,7 +7,6 @@</td>
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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;">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="LC10" 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="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</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="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">.plugin_setup</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">plugin</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">@@ -22,12 +21,12 @@ def _1(data: pd.DataFrame) -> QualityFilterStatsFmt:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="n" style="color: #333;">_stats_column_dtypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'sample-id'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff right">.</span></span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'total-input-reads'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">number</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'total-retained-reads'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">number</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-truncated'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">number</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-too-short-after-truncation'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">number</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-exceeding-maximum-ambiguous-bases'</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">number</span></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'sample-id'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'total-input-reads'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">int</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'total-retained-reads'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">int</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-truncated'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">int</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-too-short-after-truncation'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">int</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'reads-exceeding-maximum-ambiguous-bases'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff right">,</span></span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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;">" (tag: 202<span class="idiff left right">0.11.1</span>)"</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">7230c7590aa3a3400df954a6333b63f2c8c276a</span>1"</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;">"202<span class="idiff left right">0-12-05 20:44:48</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;">" (tag: 202<span class="idiff left right">1.8.0</span>)"</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">16889091c5e035dc1a849aacdb6e90b55fe096b</span>1"</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;">"202<span class="idiff left right">1-09-09 18:35:30</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2016-202<span class="idiff left right">0</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) 2016-202<span class="idiff left right">1</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2016-202<span class="idiff left right">0</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) 2016-202<span class="idiff left right">1</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/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2016-202<span class="idiff left right">0</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) 2016-202<span class="idiff left right">1</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">@@ -11,7 +11,7 @@ import gzip</td>
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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.<span class="idiff left right">util.</span>testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</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.testing</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pdt</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">qiime2</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">qiime2.sdk</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Artifact</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,8 +35,8 @@ class FilterTests(TestPluginBase):</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">package</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'q2_quality_filter.test'</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_read_fastq_seqs</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="LC38" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="s" style="color: #d14;">'@foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ATGC'</span><span class="p">,</span> <span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="s" style="color: #d14;">'IIII'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">])),</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="p">(</span><span class="s" style="color: #d14;">'@bar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGCA'</span><span class="p">,</span> <span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ABCD'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">34</span><span class="p">,</span> <span class="mi" style="color: #099;">35</span><span class="p">]))]</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">exp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="sa"><span class="idiff left">b</span></span><span class="s" style="color: #d14;">'@foo'</span><span class="p">,</span> <span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;">'ATGC'</span><span class="p">,</span> <span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="sa"><span class="idiff right">b</span></span><span class="s" style="color: #d14;">'IIII'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">,</span> <span class="mi" style="color: #099;">40</span><span class="p">])),</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="p">(</span><span class="sa"><span class="idiff left">b</span></span><span class="s" style="color: #d14;">'@bar'</span><span class="p">,</span> <span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;">'TGCA'</span><span class="p">,</span> <span class="sa"><span class="idiff">b</span></span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span> <span class="sa"><span class="idiff right">b</span></span><span class="s" style="color: #d14;">'ABCD'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mi" style="color: #099;">32</span><span class="p">,</span> <span class="mi" style="color: #099;">33</span><span class="p">,</span> <span class="mi" style="color: #099;">34</span><span class="p">,</span> <span class="mi" style="color: #099;">35</span><span class="p">]))]</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">obs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">_read_fastq_seqs</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.fastq.gz'</span><span class="p">),</span> <span class="mi" style="color: #099;">33</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">assertEqual</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">obs</span><span class="p">),</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" 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">@@ -120,8 +120,8 @@ 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="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> <span class="mf" style="color: #099;">1<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff right">.</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> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff right">.</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="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">)],</span></span>
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<pre style="margin: 0;"> <span id="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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -145,8 +145,8 @@ class FilterTests(TestPluginBase):</td>
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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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<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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<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="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> <span class="mf" style="color: #099;">1<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff right">.</span></span><span class="p">),</span></span>
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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> <span class="mf" style="color: #099;">1<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">1<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff right">.</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="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">),</span></span>
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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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)],</span></span>
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<pre style="margin: 0;"> <span id="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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<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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<pre style="margin: 0;"> <span id="LC152" 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">@@ -231,7 +231,7 @@ 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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<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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<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="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> <span class="mf" style="color: #099;">6<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">10<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">4<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff right">.</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="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)],</span></span>
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<pre style="margin: 0;"> <span id="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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -316,7 +316,7 @@ 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="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> <span class="mf" style="color: #099;">6<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">10<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">4<span class="idiff">.</span></span><span class="p">,</span> <span class="mf" style="color: #099;">0<span class="idiff right">.</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="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">,</span> <span class="mi" style="color: #099;">10</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)],</span></span>
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<pre style="margin: 0;"> <span id="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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<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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<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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<a href="https://salsa.debian.org/med-team/q2-quality-filter/-/compare/d5353dce5aa724725974b33d86b22b167eaec9a8...1d63a906cddfe182f42f6fb39aace3d9397f8a90#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) 2017-202<span class="idiff left right">0</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) 2017-202<span class="idiff left right">1</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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