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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/pycoqc">Debian Med / pycoqc</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/e378891827e12e0c8640abef031623715f03346a">e3788918</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:07:10+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/45dcaaa59a1a0255418a5a914943f8cff2c5402f">45dcaaa5</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:07:33+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Clean up rules file
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/ac7558814b315bd2002f8b57d97ec6f4efad86bd">ac755881</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:11:21+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix lintian
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/e3cca96c117e7a017070f5ead2a459464a1a158f">e3cca96c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:12:51+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/4fceccfde7f516faee87423f93165f56a0e785a0">4fceccfd</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:14:07+05:30</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/pycoqc/-/commit/ac4408fcf50d6bea2a6caa9267f7f0e4788c7bb3">ac4408fc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:14:09+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.0.23+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/de662d96ceeffedb77380b0312435df7a756bf1e">de662d96</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:14:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.5.0.23+dfsg'
Update to upstream version '2.5.0.23+dfsg'
with Debian dir baac6f2c09bf23fcd534533b6f7e45705ecc9ac7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pycoqc/-/commit/34e01da06c8d88086746b98b637c951bddedf0ff">34e01da0</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-08-19T20:14:55+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: debhelper-compat 13
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#85ccdeeb03055211183e48520592d9a93592b330">
debian/source/lintian-overrides
</a>
</li>
<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
<span class="new-file">
+
debian/tests/control
</span>
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<span class="new-file">
+
debian/tests/run-unit-test
</span>
</a>
</li>
<li class="file-stats">
<a href="#0b3e33619677413fe8f879987c9e0357046fe604">
docs/index.md
</a>
</li>
<li class="file-stats">
<a href="#a9b24c2f96ac56500918f439af04017af1e8fb62">
meta.yaml
</a>
</li>
<li class="file-stats">
<a href="#e84cecfd25f2f1f9cbf57b193c87391239a1b707">
pycoQC/Fast5_to_seq_summary.py
</a>
</li>
<li class="file-stats">
<a href="#7fb3feaa708d277c081252e8e3fa1635ac2bc2f8">
pycoQC/__init__.py
</a>
</li>
<li class="file-stats">
<a href="#9db054addcb41228e79bc5c8b1649b10f3bbc221">
pycoQC/templates/spectre.html.j2
</a>
</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</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">@@ -8,9 +8,13 @@</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![PyPI version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badge.fury.io/py/pycoQC.svg</span><span class="p">)</span>](https://badge.fury.io/py/pycoQC)</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Downloads</span><span class="p">](</span><span class="sx" style="color: #d14;">https://pepy.tech/badge/pycoqc</span><span class="p">)</span>](https://pepy.tech/project/pycoqc)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda Version</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/aleg/pycoqc/badges/version.svg</span><span class="p">)</span>](https://anaconda.org/aleg/pycoqc)</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Anaconda Downloads</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/aleg/pycoqc/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/aleg/pycoqc)</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/pycoqc/README.html)</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Bioconda Downloads</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/pycoqc/badges/downloads.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/pycoqc)</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.com/a-slide/pycoQC.svg?branch=master</span><span class="p">)</span>](https://travis-ci.com/a-slide/pycoQC)</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gh" style="color: #999;">[](https://www.codacy.com/app/a-slide/pycoQC?utm_source=github.com&utm_medium=referral&utm_content=a-slide/pycoQC&utm_campaign=Badge_Grade)</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gh" style="color: #999;">---</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown">PycoQC relies on the <span class="ge" style="font-style: italic;">*sequencing_summary.txt*</span> file generated by Albacore and Guppy, but if needed it can also generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. <span class="gs" style="font-weight: 600;">**Python 2 is not supported**</span>.</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">Great tutorial with detailed explanations by <span class="p">[</span><span class="nv" style="color: #008080;">Tim Kahlke</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/timkahlke</span><span class="p">)</span> available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"></span>
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26
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Gallery</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">summary</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/summary.gif</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">pycoqc (2.5.0.23+dfsg-1) UNRELEASED; 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"> [ Andreas Tille ]</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Remove empty reference data</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Not available in conda</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Spelling</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix conda ID</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="LC10" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Update metadata - only bioconda knows this tool</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Add autopkgtests</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Clean up rules file</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Fix lintian</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Wed, 19 Aug 2020 20:11:31 +0530</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">pycoqc (2.5.0.21+dfsg-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> * Remove totally useless test template</span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">2</span>),</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 1<span class="idiff left right">3</span>),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> python3,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools</span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,28 +4,7 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">export LC_ALL=C.UTF-8</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"># this provides:</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># DEB_SOURCE: the source package name</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"># DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"># DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"># DEB_VERSION_UPSTREAM: the package's upstream version</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext"># SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># specified by <https://reproducible-builds.org/specs/source-date-epoch/></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">export PYBUILD_NAME=pycoqc</span>
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19
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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21
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@ --with python3 --buildsystem=pybuild</span></pre>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">#ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"># do_stuff_for_testing</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">#endif</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">#get-orig-source:</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext"># . debian/get-orig-source</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#85ccdeeb03055211183e48520592d9a93592b330"><strong>debian/source/lintian-overrides</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext"># The rendered sample results are no JS without source</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">pycoqc source: source-is-missing docs/pycoQC/results*</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">pycoqc source: very-long-line-length-in-source-file docs/pycoQC/results*</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">pycoqc source: source-contains-prebuilt-javascript-object docs/pycoQC/results*</span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>pycoqc</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">CUR_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/docs/Barcode_split/data/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/docs/Fast5_to_seq_summary/data/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/docs/pycoQC/data/<span class="k" style="font-weight: 600;">*</span> <span class="nt" style="color: #000080;">-a</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rm</span> <span class="nt" style="color: #000080;">-rf</span> data</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> datafast5</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="k" style="font-weight: 600;">*</span>.fast5 datafast5</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv </span>summary_sequencing.tsv datafast5</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 1'</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Albacore-1.2.1_basecall-1D-DNA_sequencing_summary.txt <span class="se" style="color: #d14;">\</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Albacore-1.2.1_basecall-1D-DNA.html <span class="se" style="color: #d14;">\</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 2'</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Guppy-2.1.3_basecall-1D-RNA_sequencing_summary.txt <span class="se" style="color: #d14;">\</span></span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Guppy-2.1.3_basecall-1D_RNA.html <span class="se" style="color: #d14;">\</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: #000080;">-j</span> results/Guppy-2.1.3_basecall-1D_RNA.json <span class="se" style="color: #d14;">\</span></span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"></span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 3'</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Guppy-2.1.3_basecall-1D-DNA_sequencing_summary.txt <span class="se" style="color: #d14;">\</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"> <span class="nt" style="color: #000080;">-b</span> Guppy-2.1.3_basecall-1D_DNA_barcoding_summary.txt <span class="se" style="color: #d14;">\</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Guppy-2.1.3_basecall-1D_DNA_barcode.html <span class="se" style="color: #d14;">\</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="shell"></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 4'</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Albacore<span class="k" style="font-weight: 600;">*</span>RNA<span class="k" style="font-weight: 600;">*</span> <span class="se" style="color: #d14;">\</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Albacore_all_RNA.html <span class="se" style="color: #d14;">\</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="nt" style="color: #000080;">--report_title</span> <span class="s2" style="color: #d14;">"All RNA runs"</span> <span class="se" style="color: #d14;">\</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 5'</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Albacore-2.1.10_basecall-1D-DNA_sequencing_summary.txt<span class="se" style="color: #d14;">\</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Albacore-2.1.10_basecall-1D-DNA.html <span class="se" style="color: #d14;">\</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"> <span class="nt" style="color: #000080;">--min_pass_qual</span> 8 <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"> <span class="nt" style="color: #000080;">--min_pass_len</span> 200 <span class="se" style="color: #d14;">\</span></span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"> <span class="nt" style="color: #000080;">--filter_calibration</span> <span class="se" style="color: #d14;">\</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"> <span class="nt" style="color: #000080;">--min_barcode_percent</span> 10 <span class="se" style="color: #d14;">\</span></span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 6'</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">pycoQC <span class="nt" style="color: #000080;">--default_config</span> <span class="o" style="font-weight: 600;">></span> test6</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell">diff test6 pycoQC_config.json</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="shell"></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 7'</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="shell">pycoQC <span class="se" style="color: #d14;">\</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> Albacore-1.7.0_basecall-1D-DNA_sequencing_summary.txt<span class="se" style="color: #d14;">\</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> results/Albacore-1.7.0_basecall-1D-DNA.html <span class="se" style="color: #d14;">\</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="shell"> <span class="nt" style="color: #000080;">--config</span> pycoQC_config.json <span class="se" style="color: #d14;">\</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="shell"> <span class="nt" style="color: #000080;">--quiet</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="shell"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 8'</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="shell">Fast5_to_seq_summary <span class="se" style="color: #d14;">\</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> datafast5/ <span class="se" style="color: #d14;">\</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="shell"> <span class="nt" style="color: #000080;">-s</span> results/summary_sequencing.tsv</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="shell"></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="shell"><span class="nb" style="color: #0086b3;">head </span>results/summary_sequencing.tsv</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="shell"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 9'</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="shell">Fast5_to_seq_summary <span class="se" style="color: #d14;">\</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> datafast5/ <span class="se" style="color: #d14;">\</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="shell"> <span class="nt" style="color: #000080;">-s</span> results/custom_summary_sequencing.tsv <span class="se" style="color: #d14;">\</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="shell"> <span class="nt" style="color: #000080;">--verbose_level</span> 1 <span class="se" style="color: #d14;">\</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="shell"> <span class="nt" style="color: #000080;">--fields</span> mean_qscore_template called_events duration strand_score</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="shell"></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="shell"><span class="nb" style="color: #0086b3;">head </span>results/custom_summary_sequencing.tsv</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="shell"></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 10'</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="shell">Fast5_to_seq_summary <span class="se" style="color: #d14;">\</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> datafast5/ <span class="se" style="color: #d14;">\</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="shell"> <span class="nt" style="color: #000080;">-s</span> results/fn_summary_sequencing.tsv <span class="se" style="color: #d14;">\</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="shell"> <span class="nt" style="color: #000080;">--verbose_level</span> 1 <span class="se" style="color: #d14;">\</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="shell"> <span class="nt" style="color: #000080;">--include_path</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="shell"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="shell"><span class="nb" style="color: #0086b3;">head </span>results/fn_summary_sequencing.tsv</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
</pre>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 11'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="shell">Barcode_split <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> <span class="s1" style="color: #d14;">'Guppy-2.2.4-basecall-1D-DNA_sequencing_summary+barcode.txt'</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"results/"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'Test 12'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="shell">Barcode_split <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="shell"> <span class="nt" style="color: #000080;">-f</span> <span class="s2" style="color: #d14;">"Guppy-basecall-1D-DNA_sequencing_summary.txt"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="shell"> <span class="nt" style="color: #000080;">-b</span> <span class="s2" style="color: #d14;">"Guppy-basecall-1D-DNA_deepbinner_barcoding_summary.txt"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="shell"> <span class="nt" style="color: #000080;">-o</span> <span class="s2" style="color: #d14;">"results/"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="shell"> <span class="nt" style="color: #000080;">-v</span></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'PASS'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="shell"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Check if files really exist"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>f <span class="k" style="font-weight: 600;">in </span>results/<span class="k" style="font-weight: 600;">*</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="shell"><span class="k" style="font-weight: 600;">do</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="shell"> <span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> <span class="nv" style="color: #008080;">$f</span> <span class="o" style="font-weight: 600;">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="nb" style="color: #0086b3;">exit </span>1</span>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#0b3e33619677413fe8f879987c9e0357046fe604"><strong>docs/index.md</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,7 @@</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">PycoQC relies on the <span class="ge" style="font-style: italic;">*sequencing_summary.txt*</span> file generated by Albacore and Guppy, but if needed it can also generates a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices and basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. <span class="gs" style="font-weight: 600;">**Python 2 is not supported**</span>.</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown">Great tutorial with detailed explanations by <span class="p">[</span><span class="nv" style="color: #008080;">Tim Kahlke</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/timkahlke</span><span class="p">)</span> available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Gallery</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#a9b24c2f96ac56500918f439af04017af1e8fb62"><strong>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 version = "2.5.0.2<span class="idiff left right">1</span>" %</span><span class="pi">}</span></span>
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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 version = "2.5.0.2<span class="idiff left right">3</span>" %</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 name = "pycoQC" %</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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ requirements:</td>
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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;">pip>=19.2.1</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;">ripgrep>=11.0.1</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python=3.6</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python<span class="idiff left right">></span>=3.6</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">numpy=1.17.1</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">scipy=1.3.1</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;">pandas=0.25.1</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,5 +45,9 @@ test:</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">https://github.com/a-slide/pycoQC"</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">license</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GPLv3"</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">license</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">GNU</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">General</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Public</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">v3</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">(GPLv3)"</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">license_file</span><span class="pi">:</span> <span class="s" style="color: #d14;">LICENSE</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">license_family</span><span class="pi">:</span> <span class="s" style="color: #d14;">GPL</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">PycoQC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">computes</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">metrics</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">and</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">generates</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">interactive</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">QC</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">plots</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">for</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Oxford</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Nanopore</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">technologies</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">sequencing</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">data"</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_url</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">https://a-slide.github.io/pycoQC/"</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">dev_url</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">"</span></span></pre>
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<li id="e84cecfd25f2f1f9cbf57b193c87391239a1b707">
<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#e84cecfd25f2f1f9cbf57b193c87391239a1b707"><strong>pycoQC/Fast5_to_seq_summary.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">@@ -197,54 +197,73 @@ class Fast5_to_seq_summary ():</td>
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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fast5_fn</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">iter</span><span class="p">(</span><span class="n" style="color: #333;">in_q</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Try to extract data from the fast5 file</span></span>
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201
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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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202
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">h5py</span><span class="p">.</span><span class="n" style="color: #333;">File</span><span class="p">(</span><span class="n" style="color: #333;">fast5_fn</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">h5_fp</span><span class="p">:</span></span>
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define group names for current read</span></span>
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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">grp_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">"raw_read"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Raw/Reads/{}/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">h5_fp</span><span class="p">[</span><span class="s" style="color: #d14;">"/Raw/Reads"</span><span class="p">].</span><span class="n" style="color: #333;">keys</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="LC207" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_basecall"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Basecall_1D_{:03}/Summary/basecall_1d_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC208" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_calibration"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Calibration_Strand_Detection_{:03}/Summary/calibration_strand_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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209
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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_barcoding"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Barcoding_{:03}/Summary/barcoding/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"> <span class="s" style="color: #d14;">"tracking_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"UniqueGlobalKey/tracking_id"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"> <span class="s" style="color: #d14;">"channel_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"UniqueGlobalKey/channel_id"</span><span class="p">}</span></span>
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212
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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python"></span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Fetch required fields is available</span></span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fields</span><span class="p">:</span></span>
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215
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"></span>
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216
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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Special case for start time</span></span>
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217
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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"start_time"</span><span class="p">:</span></span>
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218
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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span></span>
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219
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<pre style="margin: 0;">-<span id="LC219" class="line" lang="python"> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"start_time"</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span></span>
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220
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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"start_time"</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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221
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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python"> <span class="n" style="color: #333;">sampling_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python"> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"channel_sampling_rate"</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span></span>
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223
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"channel_sampling_rate"</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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224
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start_time</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sampling_rate</span><span class="p">:</span></span>
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225
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start_time</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sampling_rate</span><span class="p">)</span></span>
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226
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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="LC227" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_not_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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="LC229" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Everything else</span></span>
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<pre style="margin: 0;">-<span id="LC230" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC231" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</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;">d</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span></span>
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<pre style="margin: 0;">-<span id="LC235" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC237" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_not_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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="LC202" class="line" lang="python"> <span class="n" style="color: #333;">multi_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'file_type'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">h5_fp</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">()</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">h5_fp</span><span class="p">.</span><span class="n" style="color: #333;">attrs</span><span class="p">[</span><span class="s" style="color: #d14;">'file_type'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b'multi-read'</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multi_read</span><span class="p">:</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="python"> <span class="n" style="color: #333;">read_ids</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;">h5_fp</span><span class="p">[</span><span class="s" style="color: #d14;">"/"</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"> <span class="n" style="color: #333;">read_ids</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;">h5_fp</span><span class="p">[</span><span class="s" style="color: #d14;">"/Raw/Reads"</span><span class="p">].</span><span class="n" style="color: #333;">keys</span><span class="p">())</span></span>
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC239" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">include_path</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">fast5_fn</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read_id</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read_ids</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Try to extract data from the fast5 file</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OrderedDict</span><span class="p">()</span></span>
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241
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Put read data in queue</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">out_q</span><span class="p">.</span><span class="n" style="color: #333;">put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"overall"</span><span class="p">][</span><span class="s" style="color: #d14;">"valid files"</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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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"overall"</span><span class="p">][</span><span class="s" style="color: #d14;">"invalid files"</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">multi_read</span><span class="p">:</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"> <span class="n" style="color: #333;">grp_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"> <span class="s" style="color: #d14;">"raw_read"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{}/Raw/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">),</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_basecall"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{read_id}/Analyses/Basecall_1D_{bc_id:03}/Summary/basecall_1d_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">bc_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_calibration"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{read_id}/Analyses/Calibration_Strand_Detection_{bc_id:03}/Summary/calibration_strand_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">bc_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_barcoding"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{read_id}/Analyses/Barcoding_{bc_id:03}/Summary/barcoding/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">read_id</span><span class="p">,</span> <span class="n" style="color: #333;">bc_id</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python"> <span class="s" style="color: #d14;">"tracking_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{}/tracking_id"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">),</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python"> <span class="s" style="color: #d14;">"channel_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/{}/channel_id"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">)}</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Define group names for current read</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="python"> <span class="n" style="color: #333;">grp_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python"> <span class="s" style="color: #d14;">"raw_read"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Raw/Reads/{}/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">read_id</span><span class="p">),</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_basecall"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Basecall_1D_{:03}/Summary/basecall_1d_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_calibration"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Calibration_Strand_Detection_{:03}/Summary/calibration_strand_template/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"> <span class="s" style="color: #d14;">"summary_barcoding"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"/Analyses/Barcoding_{:03}/Summary/barcoding/"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">basecall_id</span><span class="p">),</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="python"> <span class="s" style="color: #d14;">"tracking_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"UniqueGlobalKey/tracking_id"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"> <span class="s" style="color: #d14;">"channel_id"</span> <span class="p">:</span> <span class="s" style="color: #d14;">"UniqueGlobalKey/channel_id"</span><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python"></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Fetch required fields is available</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">field</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fields</span><span class="p">:</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="python"></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Special case for start time</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">field</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"start_time"</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;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"start_time"</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"start_time"</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python"> <span class="n" style="color: #333;">sampling_rate</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span></span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python"> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"channel_sampling_rate"</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span></span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="s" style="color: #d14;">"channel_sampling_rate"</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">start_time</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sampling_rate</span><span class="p">:</span></span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">start_time</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">sampling_rate</span><span class="p">)</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_not_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Everything else</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_get_h5_attrs</span> <span class="p">(</span></span>
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<td class="diff-line-num new new_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python"> <span class="n" style="color: #333;">fp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">h5_fp</span><span class="p">,</span> <span class="n" style="color: #333;">grp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grp_dict</span><span class="p">[</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">][</span><span class="s" style="color: #d14;">"grp"</span><span class="p">]],</span> <span class="n" style="color: #333;">attrs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">attrs_grp_dict</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">][</span><span class="s" style="color: #d14;">"attrs"</span><span class="p">])</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">v</span><span class="p">:</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="n" style="color: #333;">field</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"fields_not_found"</span><span class="p">][</span><span class="n" style="color: #333;">field</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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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="python"></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">include_path</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">d</span><span class="p">[</span><span class="s" style="color: #d14;">"path"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">fast5_fn</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="python"></span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Put read data in queue</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">d</span><span class="p">:</span></span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">out_q</span><span class="p">.</span><span class="n" style="color: #333;">put</span><span class="p">(</span><span class="n" style="color: #333;">d</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"overall"</span><span class="p">][</span><span class="s" style="color: #d14;">"valid files"</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="LC265" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"> <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="s" style="color: #d14;">"overall"</span><span class="p">][</span><span class="s" style="color: #d14;">"invalid files"</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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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"></span>
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249
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Put counter in counter queue</span></span>
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250
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;">counter_q</span><span class="p">.</span><span class="n" style="color: #333;">put</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#7fb3feaa708d277c081252e8e3fa1635ac2bc2f8"><strong>pycoQC/__init__.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.5.0.2<span class="idiff left right">1</span>'</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.5.0.2<span class="idiff left right">3</span>'</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__all__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"pycoQC"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Fast5_to_seq_summary"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Barcode_split"</span><span class="p">,</span> <span class="s" style="color: #d14;">"common"</span><span class="p">]</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#9db054addcb41228e79bc5c8b1649b10f3bbc221"><strong>pycoQC/templates/spectre.html.j2</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">@@ -68,10 +68,6 @@</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="html"> {{ src_files }}</span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="html"> <span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="html"> <span class="nt" style="color: #000080;"></div></span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="html"></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="html"> <span class="c" style="color: #998; font-style: italic;"><!-- <div class="column col-12 col-mx-auto text-center"></span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> <h6>SHA256: {{ summary_file_hash }}</h6></span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="html"><span class="c" style="color: #998; font-style: italic;"> </div> --></span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/compare/bd4675360e91d6c48c45ed7eba5124982f08552f...34e01da06c8d88086746b98b637c951bddedf0ff#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ from setuptools import setup</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Define package info</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"pycoQC"</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.5.0.2<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.5.0.2<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data"</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">"README.md"</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fh</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fh</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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