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<h3>
Nilesh Patra pushed to branch upstream
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/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43">b46d0d7f</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-20T18:03:32+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.5.2+dfsg</pre>
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<h4>27 changed files:</h4>
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<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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.versipy/README.md
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.versipy/__init__.py
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.versipy/mkdocs.yml
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.versipy/setup.py
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README.md
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<a href="#169871d3b9351ebd69c81f84a0e87f9fd9772be2">
deploy_anaconda.sh
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docs/index.md
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docs/installation.md
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<a href="#49ca3aa11c1cafc36444688743f9371d79d5044a">
docs/pycoQC/CLI_usage.ipynb
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<a href="#5c9789bd13fad7443f2bdb7fbf28b9e3b3086ce7">
docs/pycoQC/results/Albacore-1.2.1_basecall-1D-DNA.html
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<a href="#a1d3728ce815cf05c6eee0539ec2abae09439c59">
docs/pycoQC/results/Albacore-2.1.10_basecall-1D-DNA.html
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docs/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.html
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docs/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.json
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docs/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.html
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<a href="#50849afd4e4170b36b4b962754237c3c246f8519">
docs/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.json
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<a href="#a9b24c2f96ac56500918f439af04017af1e8fb62">
meta.yaml
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mkdocs.yml
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pycoQC/__init__.py
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pycoQC/__main__.py
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pycoQC/pycoQC.py
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pycoQC/pycoQC_report.py
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setup.py
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versipy_history.txt
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<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@ dist: xenial</td>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.6</span></span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">branches</span><span class="pi">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">only</span></span><span class="pi">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;"><span class="idiff left right">except</span></span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">master</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">dev</span></span>
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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,6 +11,8 @@ install:</td>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install nbconvert requests jinja2 mkdocs mkdocs-material pygments pymdown-extensions mkdocs-exclude</span></span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Install this one after or it raises an error</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install mknotebooks</span></span>
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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Fix temp issue with pypi deployment</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">
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pip install keyring==21.4.0</span></span>
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<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"></span>
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<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,45 +21,68 @@ before_deploy:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdocs build --verbose --clean</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">deploy</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Deploy mkdoc documentation to github page</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pages</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">target_branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">gh-pages-test</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">github_token</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$GH_TOKEN"</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">local_dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">site</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">dev</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Development / test deployment</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pages</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">target_branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">gh-pages-test</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">github_token</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$GH_TOKEN"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">local_dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">site</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">master</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG == *.dev*</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Deploy package to pypy</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">aleg</span></span>
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41
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$PYPI_PW"</span></span>
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42
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">server</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://test.pypi.org/legacy/</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">dev</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG == *.dev*</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">script</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash ./deploy_anaconda.sh $ANACONDA_DEV_TOKEN</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG == *.dev*</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Production version deployment</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pages</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">target_branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">gh-pages-test</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">github_token</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$GH_TOKEN"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="na" style="color: #008080;">local_dir</span><span class="pi">:</span> <span class="s" style="color: #d14;">site</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</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="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG != *.dev*</span></span>
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45
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="yaml"></span>
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46
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">pypi</span></span>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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47
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<td class="diff-line-num new_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">aleg</span></span>
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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
48
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<td class="diff-line-num new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="yaml"> <span class="na" style="color: #008080;">password</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$PYPI_PW"</span></span>
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49
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">master</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG != *.dev*</span></span>
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51
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="yaml"></span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Deploy to Anaconda</span></span>
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53
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<td class="diff-line-num new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">script</span></span>
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54
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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
55
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<td class="diff-line-num new_line old" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash ./deploy_anaconda.sh $ANACONDA_<span class="idiff left right">DEV_</span>TOKEN</span></span>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash ./deploy_anaconda.sh $ANACONDA_TOKEN</span></span>
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56
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">dev</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG != *.dev*</span></span>
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58
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">script</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">provider</span><span class="pi">:</span> <span class="s" style="color: #d14;">releases</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="yaml"> <span class="na" style="color: #008080;">api_key</span><span class="pi">:</span> <span class="s" style="color: #d14;">$GH_TOKEN</span></span>
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="yaml"> <span class="na" style="color: #008080;">skip_cleanup</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s" style="color: #d14;">bash ./deploy_anaconda.sh $ANACONDA_TOKEN</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="yaml"> <span class="na" style="color: #008080;">on</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">master</span></span></pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="yaml"> <span class="na" style="color: #008080;">all_branches</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="yaml"> <span class="na" style="color: #008080;">condition</span><span class="pi">:</span> <span class="s" style="color: #d14;">$TRAVIS_TAG != *.dev*</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#93d67e99a464ab0252f5fefde5276b5f53c9d05a"><strong>.versipy/README.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># __package_name__ v__package_version__</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">pycoQC</span><span class="p">](</span><span class="sx" style="color: #d14;">https://raw.githubusercontent.com/a-slide/pycoQC/master/docs/pictures/pycoQC_long.png</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![JOSS</span><span class="p">](</span><span class="sx" style="color: #d14;">http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa/status.svg</span><span class="p">)</span>](http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa)</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zenodo.org/badge/94531811.svg</span><span class="p">)</span>](https://zenodo.org/badge/latestdoi/94531811)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Gitter chat</span><span class="p">](</span><span class="sx" style="color: #d14;">https://badges.gitter.im/gitterHQ/gitter.png</span><span class="p">)</span>](https://gitter.im/pycoQC/community?utm_source=share-link&utm_medium=link&utm_campaign=share-link)</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![GitHub license</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/license/a-slide/pycoQC.svg</span><span class="p">)</span>](https://github.com/a-slide/pycoQC/blob/master/LICENSE)</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;">![Language</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/Language-Python3.6+-yellow.svg</span><span class="p">)</span>](https://www.python.org/)</span>
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<pre style="margin: 0;">+<span id="LC11" 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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<pre style="margin: 0;">+<span id="LC12" 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="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC14" 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="LC15" 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="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" 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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18
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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;">![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="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC20" 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="LC21" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Codacy Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://api.codacy.com/project/badge/Grade/07db58961a3c4fc1b6dc34c54079b477</span><span class="p">)</span>](https://www.codacy.com/app/a-slide/pycoQC?utm_source=github.com<span class="ni" style="color: #800080;">&</span>utm_medium=referral<span class="ni" style="color: #800080;">&</span>utm_content=a-slide/pycoQC<span class="ni" style="color: #800080;">&</span>utm_campaign=Badge_Grade)</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**__package_description__**</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__package_introduction__</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown">Full documentation is available at __package_doc_url__</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC31" 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 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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">reads_len_1D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/reads_len_1D.gif</span><span class="p">)</span>]</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">reads_len_1D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/reads_qual_1D.gif</span><span class="p">)</span>]</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">reads_qual_len_2D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/reads_qual_len_2D.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">channels_activity</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/channels_activity.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">output_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/output_over_time.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">qual_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/qual_over_time.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">len_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/len_over_time.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_len</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/align_len_1D.gif</span><span class="p">)</span></span>
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50
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_score</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/align_score_1D.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_score_len_2D</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/align_score_len_2D.gif</span><span class="p">)</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_coverage</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/alignment_coverage.gif</span><span class="p">)</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_rate</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/alignment_rate.gif</span><span class="p">)</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_summary</span><span class="p">](</span><span class="sx" style="color: #d14;">./docs/pictures/alignment_summary.gif</span><span class="p">)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example HTML reports</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></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="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore_all_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore_all_RNA.html</span><span class="p">)</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.html</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="67" 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">
67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.3_basecall-1D_alignment-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.html</span><span class="p">)</span></span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="69" 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">
69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.2.1_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.2.1_basecall-1D-DNA.html</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_DNA_barcode</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_DNA_barcode.html</span><span class="p">)</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="73" 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">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA_API</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.html</span><span class="p">)</span></span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="75" 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">
75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-2.1.10_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-2.1.10_basecall-1D-DNA.html</span><span class="p">)</span></span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example JSON reports</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.3_basecall-1D_alignment-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.json</span><span class="p">)</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.json</span><span class="p">)</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA_API</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.json</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Disclaimer</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown">Please be aware that pycoQC is a research package that is still under development.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown">It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">Thank you</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Classifiers</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="p">*</span> __classifiers_1__</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="p">*</span> __classifiers_2__</span>
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<td class="diff-line-num new new_line" data-linenumber="100" 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">
100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">*</span> __classifiers_3__</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">*</span> __classifiers_4__</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="p">*</span> __classifiers_5__</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## licence</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__package_licence__</span> (__package_licence_url__)</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown">Copyright © 2020 __author_name__</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Authors</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="p">*</span> __author_name__ / __author_email__ / __author_url__</span></pre>
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<li id="72af91bf4b9036becca6ae69c8f34caa072fb929">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#72af91bf4b9036becca6ae69c8f34caa072fb929"><strong>.versipy/__init__.py</strong></a>
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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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<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;">__name__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__package_name__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__package_version__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__description__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__package_description__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="n" style="color: #333;">__url__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__package_url__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__licence__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__package_licence__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"__author_name__"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" 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/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#baca5a5397ce4afb4e50585d922347d29fd1898a"><strong>.versipy/index.md</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Welcome to __package_name__ v__package_version__ documentation</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">logo</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/pycoQC_long.svg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**__package_description__**</span></span>
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6
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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"><span class="gs" style="font-weight: 600;">__package_introduction__</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Gallery</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" 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;">pictures/summary.gif</span><span class="p">)</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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13
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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;">reads_len_1D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/reads_len_1D.gif</span><span class="p">)</span>]</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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15
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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;">reads_len_1D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/reads_qual_1D.gif</span><span class="p">)</span>]</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">reads_qual_len_2D_example</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/reads_qual_len_2D.gif</span><span class="p">)</span></span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">channels_activity</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/channels_activity.gif</span><span class="p">)</span></span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"></span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">output_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/output_over_time.gif</span><span class="p">)</span></span>
</pre>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">qual_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/qual_over_time.gif</span><span class="p">)</span></span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">len_over_time</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/len_over_time.gif</span><span class="p">)</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="27" 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">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_len</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/align_len_1D.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_score</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/align_score_1D.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">align_score_len_2D</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/align_score_len_2D.gif</span><span class="p">)</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_coverage</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/alignment_coverage.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_rate</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/alignment_rate.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">alignment_summary</span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/alignment_summary.gif</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example HTML reports</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore_all_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore_all_RNA.html</span><span class="p">)</span></span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.html</span><span class="p">)</span></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.3_basecall-1D_alignment-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.html</span><span class="p">)</span></span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.2.1_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.2.1_basecall-1D-DNA.html</span><span class="p">)</span></span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_DNA_barcode</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_DNA_barcode.html</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA_API</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-2.1.10_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-2.1.10_basecall-1D-DNA.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA.html</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Example JSON reports</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.3_basecall-1D_alignment-DNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.json</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Guppy-2.1.3_basecall-1D_RNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.json</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA_API</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.json</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#96a52552647ccd44ce65a1543b0ab0bf33e3acd3"><strong>.versipy/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 = "__package_version__" %</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 = "__package_name__" %</span><span class="pi">}</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">package</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">name|lower</span> <span class="pi">}}</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="pi">{{</span> <span class="nv" style="color: #008080;">version</span> <span class="pi">}}</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">source</span><span class="pi">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">dist/{{ name }}-{{ version }}.tar.gz</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">number</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pip</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">install</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">{{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">name</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}-{{</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">version</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">}}.tar.gz</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">--no-deps</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">--ignore-installed</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-vv</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">entry_points</span><span class="pi">:</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__entry_point_1__</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__entry_point_2__</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__entry_point_3__</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">noarch</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">python"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">requirements</span><span class="pi">:</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python__minimal_python__</span></span>
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23
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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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24
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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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25
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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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26
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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;">__dependency_1__</span></span>
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27
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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;">__dependency_2__</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__dependency_3__</span></span>
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29
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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;">__dependency_4__</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__dependency_5__</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__dependency_6__</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__dependency_7__</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">__dependency_8__</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">imports</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pycoQC.pycoQC</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pycoQC.Fast5_to_seq_summary</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pycoQC.Barcode_split</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">commands</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pycoQC --help</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">Fast5_to_seq_summary --help</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">Barcode_split --help</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_url__</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_doc_url__</span></span>
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48
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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="s" style="color: #d14;">__package_licence__</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">licence_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_licence_url__</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_description__</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"><span class="na" style="color: #008080;">extra</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">author</span><span class="pi">:</span> <span class="s" style="color: #d14;">__author_name__</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">author_email</span><span class="pi">:</span> <span class="s" style="color: #d14;">__author_email__</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">author_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">__author_url__</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#3fa4d17ca5aaea7816fe1354a67ea03d37437756"><strong>.versipy/mkdocs.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Project information</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">site_name</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_name__</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">site_description</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_description__</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">site_author</span><span class="pi">:</span> <span class="s" style="color: #d14;">__author_name__</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">site_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_doc_url__</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Repository</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">repo_name</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">a-slide/pycoQC'</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">repo_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">__package_url__</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Copyright</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">copyright</span><span class="pi">:</span> <span class="s" style="color: #d14;">Copyright © 2020 __author_name__</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Navigation menu</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">nav</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Home</span><span class="pi">:</span> <span class="s" style="color: #d14;">index.md</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Installation instructions</span><span class="pi">:</span> <span class="s" style="color: #d14;">installation.md</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">pycoQC Usage</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Using pycoQC</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC/usage.md</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">jupyter API usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC/API_usage.ipynb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Command line usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC/CLI_usage.ipynb</span></span>
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Barcode_split Usage</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Using Barcode_split</span><span class="pi">:</span> <span class="s" style="color: #d14;">Barcode_split/usage.md</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">jupyter API usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">Barcode_split/API_usage.ipynb</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Command line usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">Barcode_split/CLI_usage.ipynb</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Fast5_to_seq_summary Usage</span><span class="pi">:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Using Fast5_to_seq_summary</span><span class="pi">:</span> <span class="s" style="color: #d14;">Fast5_to_seq_summary/usage.md</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">jupyter API usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">Fast5_to_seq_summary/API_usage.ipynb</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Command line usage</span><span class="pi">:</span> <span class="s" style="color: #d14;">Fast5_to_seq_summary/CLI_usage.ipynb</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Citing pycoQC</span><span class="pi">:</span> <span class="s" style="color: #d14;">citing.md</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Acknowledgements</span><span class="pi">:</span> <span class="s" style="color: #d14;">acknowledgements.md</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Alternative and complementary packages</span><span class="pi">:</span> <span class="s" style="color: #d14;">alternative.md</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Contributing Guidelines</span><span class="pi">:</span> <span class="s" style="color: #d14;">contributing.md</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Code of conduct</span><span class="pi">:</span> <span class="s" style="color: #d14;">code_of_conduct.md</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Licence</span><span class="pi">:</span> <span class="s" style="color: #d14;">licence.md</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">Changelog</span><span class="pi">:</span> <span class="s" style="color: #d14;">changelog.md</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Theme customization</span></span>
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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"><span class="na" style="color: #008080;">theme</span><span class="pi">:</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">material'</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">highlightjs</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">font</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"></span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"><span class="na" style="color: #008080;">markdown_extensions</span><span class="pi">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">admonition</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">codehilite</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.betterem</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">smart_enable</span><span class="pi">:</span> <span class="s" style="color: #d14;">all</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.caret</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.critic</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.details</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.emoji</span><span class="pi">:</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">emoji_generator</span><span class="pi">:</span> <span class="kt" style="color: #458; font-weight: 600;">!!python/name:pymdownx.emoji.to_svg</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.inlinehilite</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.magiclink</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">repo_url_shorthand</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="yaml"> <span class="na" style="color: #008080;">user</span><span class="pi">:</span> <span class="s" style="color: #d14;">a-slide</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="yaml"> <span class="na" style="color: #008080;">repo</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.mark</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.smartsymbols</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.superfences</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.tasklist</span><span class="pi">:</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="yaml"> <span class="na" style="color: #008080;">custom_checkbox</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pymdownx.tilde</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"><span class="na" style="color: #008080;">plugins</span><span class="pi">:</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mknotebooks</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#1f8372d5b14953c58906cfc6fb65064e474ab1a5"><strong>.versipy/setup.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!python3</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="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="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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8
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<pre style="margin: 0;">+<span id="LC8" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__package_name__'</span><span class="p">,</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" 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;">'__package_description__'</span><span class="p">,</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__package_version__'</span><span class="p">,</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'text/markdown'</span><span class="p">,</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__package_url__'</span><span class="p">,</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__author_name__'</span><span class="p">,</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__author_email__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">license</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'__package_licence__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">python_requires</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'__minimal_python__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'__classifiers_1__'</span><span class="p">,</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'__classifiers_2__'</span><span class="p">,</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"> <span class="s" style="color: #d14;">'__classifiers_3__'</span><span class="p">,</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'__classifiers_4__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'__classifiers_5__'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_1__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_2__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_3__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_4__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_5__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_6__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_7__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'__dependency_8__'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'__package_name__'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'__package_name__'</span><span class="p">:</span> <span class="s" style="color: #d14;">'__package_name__'</span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'__package_name__'</span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'templates/*'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'__entry_point_1__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="s" style="color: #d14;">'__entry_point_2__'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">'__entry_point_3__'</span><span class="p">]}</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># pycoQC v2.5.2</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">pycoQC</span><span class="p">](</span><span class="sx" style="color: #d14;">https://raw.githubusercontent.com/a-slide/pycoQC/master/docs/pictures/pycoQC_long.png</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![JOSS</span><span class="p">](</span><span class="sx" style="color: #d14;">http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa/status.svg</span><span class="p">)</span>](http://joss.theoj.org/papers/ea8e08dc950622bdd5d16a65649954aa)</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">@@ -17,17 +19,14 @@</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC20" 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="LC21" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Codacy Badge</span><span class="p">](</span><span class="sx" style="color: #d14;">https://api.codacy.com/project/badge/Grade/07db58961a3c4fc1b6dc34c54079b477</span><span class="p">)</span>](https://www.codacy.com/app/a-slide/pycoQC?utm_source=github.com<span class="ni" style="color: #800080;">&</span>utm_medium=referral<span class="ni" style="color: #800080;">&</span>utm_content=a-slide/pycoQC<span class="ni" style="color: #800080;">&</span>utm_campaign=Badge_Grade)</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="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Full documentation is available at https://a-slide.github.io/pycoQC/**</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**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="LC26" class="line" lang="markdown"></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 generate<span class="idiff left">s 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><span class="gs" style="font-weight: 600;"><span class="idiff">**Python 2 is not supported**</span></span><span class="idiff right">.</span></span>
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<pre style="margin: 0;">+<span id="LC27" 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 generate<span class="idiff left"> a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices, basecalled with Albacore 1.2.1+ or Guppy 2.1.3+. PycoQC is written in pure Python3. </span><span class="gs" style="font-weight: 600;"><span class="idiff">**Python 2 is not supported**</span></span><span class="idiff">. For a quick introduction see tutorial by </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Tim Kahlke</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/timkahlke</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="idiff left">Great tutorial with detailed explanations by </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Tim Kahlke</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://github.com/timkahlke</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right"> available at https://timkahlke.github.io/LongRead_tutorials/QC_P.html</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="idiff left right">Full documentation is available at https://adrienleger.com/pycoQC</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" 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="LC32" class="line" lang="markdown"></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">@@ -85,8 +84,29 @@ Great tutorial with detailed explanations by [Tim Kahlke](https://github.com/tim</td>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">Albacore-1.7.0_basecall-1D-DNA_API</span><span class="p">](</span><span class="sx" style="color: #d14;">https://a-slide.github.io/pycoQC/pycoQC/results/Albacore-1.7.0_basecall-1D-DNA_API.json</span><span class="p">)</span></span>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Authors</span></span>
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="p">*</span> Adrien Leger - aleg {at} ebi.ac.uk</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Disclaimer</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown">Please be aware that pycoQC is a research package that is still under development.</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown">It was tested under Linux Ubuntu 16.04 and in an HPC environment running under Red Hat Enterprise 7.1.</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">Thank you</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"></span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Classifiers</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"></span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown"><span class="p">*</span> Development Status :: 3 - Alpha</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="p">*</span> Intended Audience :: Science/Research</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"><span class="p">*</span> Topic :: Scientific/Engineering :: Bio-Informatics</span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">*</span> License :: OSI Approved :: GNU General Public License v3 (GPLv3)</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="p">*</span> Programming Language :: Python :: 3</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## licence</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown">GPLv3 (https://www.gnu.org/licenses/gpl-3.0.en.html)</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown">Copyright © 2020 Adrien Leger & Tommaso Leonardi</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Authors</span></span>
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">Tommaso Leonardi - tom {at} tleo.io</span></span></pre>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown"><span class="p">*</span> <span class="idiff left right">Adrien Leger & Tommaso Leonardi / aleg@ebi.ac.uk / https://adrienleger.com</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#169871d3b9351ebd69c81f84a0e87f9fd9772be2"><strong>deploy_anaconda.sh</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ echo "compile package from setup.py"</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell">python setup.py sdist</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Build noarch package..."</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="shell">conda build meta.yaml <span class="nt" style="color: #000080;">--python</span> 3.6 <span class="nt" style="color: #000080;">--numpy</span> 1.1 <span class="nt" style="color: #000080;">--output-folder</span> conda_build <span class="nt" style="color: #000080;">-c</span> bioconda <span class="nt" style="color: #000080;">-c</span> conda-forge</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">conda build meta.yaml <span class="nt" style="color: #000080;">--python</span> 3.6 <span class="nt" style="color: #000080;">--numpy</span> 1.1 <span class="nt" style="color: #000080;">--output-folder</span> conda_build <span class="nt" style="color: #000080;">-c</span> bioconda <span class="nt" style="color: #000080;">-c</span> conda-forge<span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff right">--no-include-recipe</span></span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="shell"></span>
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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="s2" style="color: #d14;">"Deploying to Anaconda.org..."</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell">anaconda <span class="nt" style="color: #000080;">-v</span> <span class="nt" style="color: #000080;">-t</span> <span class="nv" style="color: #008080;">$1</span> upload conda_build/<span class="k" style="font-weight: 600;">**</span>/<span class="k" style="font-weight: 600;">*</span>.tar.bz2</span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#0b3e33619677413fe8f879987c9e0357046fe604"><strong>docs/index.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Welcome to pycoQC documentation</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Welcome to pycoQC <span class="idiff left right">v2.5.2 </span>documentation</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;"><span class="idiff left right">summary</span></span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/pycoQC_long.svg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;"><span class="idiff left right">logo</span></span><span class="p">](</span><span class="sx" style="color: #d14;">pictures/pycoQC_long.svg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**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="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="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 generate a summary file from basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion, Gridion and Promethion devices, 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>. For a quick introduction see tutorial 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="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Gallery</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#55199a4dc06a52cf6712fdb7406566e3a77fd28f"><strong>docs/installation.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">@@ -52,13 +52,13 @@ pip install --index-url https://test.pypi.org/simple/ pycoQC -U</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"># First installation</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown">conda <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-c</span> aleg <span class="nv" style="color: #008080;">pycoqc</span><span class="o" style="font-weight: 600;">=[</span>VERSION]</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown">conda <span class="nb" style="color: #0086b3;">install</span> <span class="nt" style="color: #000080;">-c</span> aleg <span class="nt" style="color: #000080;"><span class="idiff left">-c</span></span><span class="idiff"> anaconda </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> bioconda </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff right"> conda-forge </span><span class="nv" style="color: #008080;">pycoqc</span><span class="o" style="font-weight: 600;">=[</span>VERSION]</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown">You can also get the <span class="gs" style="font-weight: 600;">**unstable**</span> development version from my dev channel</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown">conda <span class="idiff left">update </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff right"> aleg_dev</span> <span class="nv" style="color: #008080;">pycoqc</span><span class="o" style="font-weight: 600;">=[</span>VERSION]</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown">conda <span class="nb" style="color: #0086b3;"><span class="idiff left">install</span></span><span class="idiff"> </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> aleg_dev </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> anaconda </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff"> bioconda </span><span class="nt" style="color: #000080;"><span class="idiff">-c</span></span><span class="idiff right"> conda-forge</span> <span class="nv" style="color: #008080;">pycoqc</span><span class="o" style="font-weight: 600;">=[</span>VERSION]</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Option 3: Installation with pip from Github</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#49ca3aa11c1cafc36444688743f9371d79d5044a"><strong>docs/pycoQC/CLI_usage.ipynb</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">@@ -39,8 +39,8 @@</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> "execution_count": 2,</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"> "metadata": {</span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"> "ExecuteTime": {</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:03:45.519891</span>Z",</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:03:44.701501</span>Z"</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:25.978368</span>Z",</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:25.675755</span>Z"</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> },</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> "init_cell": true</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> },</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">@@ -60,8 +60,8 @@</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> ],</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> "source": [</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext"> "# Using <span class="idiff left right">virtualenvwrapper here but can also be done with Conda</span> \n",</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext"> "<span class="idiff left right">workon</span> pycoQC"</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> "# Using <span class="idiff left right">conda here but can also be done with other virtenv managers</span> \n",</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> "<span class="idiff left right">conda activate</span> pycoQC"</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"> ]</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"> },</span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"> {</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,8 +76,8 @@</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> "execution_count": 3,</span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"> "metadata": {</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"> "ExecuteTime": {</span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:03:48.456722</span>Z",</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:03:46.112199</span>Z"</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:29.434767</span>Z",</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:27.842415</span>Z"</span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> },</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> "init_cell": true</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> },</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,8 +95,8 @@</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"> " [--filter_calibration] [--filter_duplicated]\n",</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"> " [--min_barcode_percent MIN_BARCODE_PERCENT]\n",</span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"> " [--report_title REPORT_TITLE] [--template_file TEMPLATE_FILE]\n",</span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="plaintext"> " [--config_file CONFIG_FILE] [--s<span class="idiff left right">ample SAMPLE] [--default_config</span>]\n",</span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="plaintext"> " [-v | -q]\n",</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> " [--config_file CONFIG_FILE] [--s<span class="idiff left right">kip_coverage_plot</span>]\n",</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> " [-<span class="idiff left right">-sample SAMPLE] [--default_config] [-</span>v | -q]\n",</span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"> "\n",</span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext"> "pycoQC computes metrics and generates interactive QC plots from the sequencing summary\n",</span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="plaintext"> "report generated by Oxford Nanopore technologies basecallers\n",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -170,6 +170,9 @@</td>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext"> " are the names of the plots to be included. The second\n",</span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext"> " level keys are the parameters to pass to each plotting\n",</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="plaintext"> " function (default: )\")\n",</span>
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<td class="diff-line-num new old_line" data-linenumber="173" 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="LC173" class="line" lang="plaintext"> " --skip_coverage_plot Skip the coverage plot in HTML report. Useful when\n",</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"> " using a reference file containing many sequences, i.e.\n",</span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext"> " transcriptome (default: False)\n",</span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="plaintext"> "\n",</span>
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174
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext"> "Other options:\n",</span>
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175
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext"> " --sample SAMPLE If not None a n number of reads will be randomly\n",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -207,11 +210,11 @@</td>
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207
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210
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext"> },</span>
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208
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211
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"> {</span>
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209
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"> "cell_type": "code",</span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">5</span>,</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">4</span>,</span>
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211
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214
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="plaintext"> "metadata": {</span>
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212
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215
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="plaintext"> "ExecuteTime": {</span>
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213
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<pre style="margin: 0;">-<span id="LC213" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:11:40.671213</span>Z",</span>
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214
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:11:33.658799</span>Z"</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:38.267960</span>Z",</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:32.382173</span>Z"</span>
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215
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="plaintext"> },</span>
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216
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="plaintext"> "scrolled": false</span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="plaintext"> },</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -263,11 +266,11 @@</td>
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext"> },</span>
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264
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext"> {</span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="plaintext"> "cell_type": "code",</span>
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<pre style="margin: 0;">-<span id="LC266" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">6</span>,</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">5</span>,</span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="plaintext"> "metadata": {</span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="plaintext"> "ExecuteTime": {</span>
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:11:49.711200</span>Z",</span>
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:11:42.841120</span>Z"</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:46.326442</span>Z",</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:40.149501</span>Z"</span>
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271
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="plaintext"> },</span>
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="plaintext"> "scrolled": false</span>
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="plaintext"> },</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -318,35 +321,15 @@</td>
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318
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321
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="plaintext"> },</span>
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319
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322
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<pre style="margin: 0;"> <span id="LC322" class="line" lang="plaintext"> {</span>
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320
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323
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<pre style="margin: 0;"> <span id="LC323" class="line" lang="plaintext"> "cell_type": "code",</span>
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321
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<pre style="margin: 0;">-<span id="LC321" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">7</span>,</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">null</span>,</span>
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322
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325
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="plaintext"> "metadata": {</span>
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323
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326
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="plaintext"> "ExecuteTime": {</span>
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324
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:12:03.752064</span>Z",</span>
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<pre style="margin: 0;">-<span id="LC325" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:11:56.394286</span>Z"</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:46.328458</span>Z",</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:43.632</span>Z"</span>
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326
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329
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="plaintext"> },</span>
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327
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330
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<pre style="margin: 0;"> <span id="LC330" class="line" lang="plaintext"> "scrolled": false</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
328
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331
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="plaintext"> },</span>
</pre>
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329
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<pre style="margin: 0;">-<span id="LC329" class="line" lang="plaintext"> "outputs": [</span>
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330
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="plaintext"> {</span>
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331
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<pre style="margin: 0;">-<span id="LC331" class="line" lang="plaintext"> "name": "stdout",</span>
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332
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<pre style="margin: 0;">-<span id="LC332" class="line" lang="plaintext"> "output_type": "stream",</span>
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333
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="plaintext"> "text": [</span>
</pre>
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<pre style="margin: 0;">-<span id="LC334" class="line" lang="plaintext"> "Checking arguments values\n",</span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="plaintext"> "Check input data files\n",</span>
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<pre style="margin: 0;">-<span id="LC336" class="line" lang="plaintext"> "Parse data files\n",</span>
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<pre style="margin: 0;">-<span id="LC337" class="line" lang="plaintext"> "Merge data\n",</span>
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<pre style="margin: 0;">-<span id="LC338" class="line" lang="plaintext"> "Cleaning data\n",</span>
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<pre style="margin: 0;">-<span id="LC339" class="line" lang="plaintext"> "Loading plotting interface\n",</span>
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<pre style="margin: 0;">-<span id="LC340" class="line" lang="plaintext"> "(pycoQC) "</span>
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<pre style="margin: 0;">-<span id="LC341" class="line" lang="plaintext"> ]</span>
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<pre style="margin: 0;">-<span id="LC342" class="line" lang="plaintext"> },</span>
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<pre style="margin: 0;">-<span id="LC343" class="line" lang="plaintext"> {</span>
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344
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<pre style="margin: 0;">-<span id="LC344" class="line" lang="plaintext"> "ename": "",</span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext"> "evalue": "1",</span>
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<pre style="margin: 0;">-<span id="LC346" class="line" lang="plaintext"> "output_type": "error",</span>
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<pre style="margin: 0;">-<span id="LC347" class="line" lang="plaintext"> "traceback": []</span>
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348
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<pre style="margin: 0;">-<span id="LC348" class="line" lang="plaintext"> }</span>
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349
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<pre style="margin: 0;">-<span id="LC349" class="line" lang="plaintext"> ],</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext"> "outputs": [],</span>
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<pre style="margin: 0;"> <span id="LC333" class="line" lang="plaintext"> "source": [</span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="plaintext"> "pycoQC \\\n",</span>
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352
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335
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<pre style="margin: 0;"> <span id="LC335" class="line" lang="plaintext"> " -f ./data/Guppy-2.1.3_basecall-1D-DNA_sequencing_summary.txt.gz \\\n",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -371,35 +354,15 @@</td>
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext"> },</span>
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372
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext"> {</span>
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373
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="plaintext"> "cell_type": "code",</span>
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374
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<pre style="margin: 0;">-<span id="LC374" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">8</span>,</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">null</span>,</span>
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375
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358
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<pre style="margin: 0;"> <span id="LC358" class="line" lang="plaintext"> "metadata": {</span>
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376
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="plaintext"> "ExecuteTime": {</span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:12:12.791372</span>Z",</span>
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378
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<pre style="margin: 0;">-<span id="LC378" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:12:05.157406</span>Z"</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:46.329661</span>Z",</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:45.948</span>Z"</span>
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379
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362
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<pre style="margin: 0;"> <span id="LC362" class="line" lang="plaintext"> },</span>
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380
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363
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<pre style="margin: 0;"> <span id="LC363" class="line" lang="plaintext"> "scrolled": false</span>
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381
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="plaintext"> },</span>
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382
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<pre style="margin: 0;">-<span id="LC382" class="line" lang="plaintext"> "outputs": [</span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="plaintext"> {</span>
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384
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<pre style="margin: 0;">-<span id="LC384" class="line" lang="plaintext"> "name": "stdout",</span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="plaintext"> "output_type": "stream",</span>
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<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
386
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<pre style="margin: 0;">-<span id="LC386" class="line" lang="plaintext"> "text": [</span>
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<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
387
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<pre style="margin: 0;">-<span id="LC387" class="line" lang="plaintext"> "Checking arguments values\n",</span>
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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
388
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<pre style="margin: 0;">-<span id="LC388" class="line" lang="plaintext"> "Check input data files\n",</span>
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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="plaintext"> "Parse data files\n",</span>
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390
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<pre style="margin: 0;">-<span id="LC390" class="line" lang="plaintext"> "Merge data\n",</span>
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391
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<pre style="margin: 0;">-<span id="LC391" class="line" lang="plaintext"> "Cleaning data\n",</span>
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<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
392
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<pre style="margin: 0;">-<span id="LC392" class="line" lang="plaintext"> "Loading plotting interface\n",</span>
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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
393
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<pre style="margin: 0;">-<span id="LC393" class="line" lang="plaintext"> "(pycoQC) "</span>
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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
394
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<pre style="margin: 0;">-<span id="LC394" class="line" lang="plaintext"> ]</span>
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395
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<pre style="margin: 0;">-<span id="LC395" class="line" lang="plaintext"> },</span>
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<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
396
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<pre style="margin: 0;">-<span id="LC396" class="line" lang="plaintext"> {</span>
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<td class="diff-line-num old old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="plaintext"> "ename": "",</span>
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<td class="diff-line-num old old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
398
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<pre style="margin: 0;">-<span id="LC398" class="line" lang="plaintext"> "evalue": "1",</span>
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<td class="diff-line-num old old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
399
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="plaintext"> "output_type": "error",</span>
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<td class="diff-line-num old old_line" data-linenumber="400" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
400
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<pre style="margin: 0;">-<span id="LC400" class="line" lang="plaintext"> "traceback": []</span>
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401
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<pre style="margin: 0;">-<span id="LC401" class="line" lang="plaintext"> }</span>
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402
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="plaintext"> ],</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext"> "outputs": [],</span>
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403
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366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="plaintext"> "source": [</span>
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404
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367
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<pre style="margin: 0;"> <span id="LC367" class="line" lang="plaintext"> "pycoQC \\\n",</span>
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405
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="plaintext"> " -f ./data/Albacore*RNA* \\\n",</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="433" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -433,11 +396,11 @@</td>
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433
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396
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="plaintext"> },</span>
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434
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397
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="plaintext"> {</span>
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435
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398
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="plaintext"> "cell_type": "code",</span>
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436
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<pre style="margin: 0;">-<span id="LC436" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">9</span>,</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">6</span>,</span>
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437
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400
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="plaintext"> "metadata": {</span>
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438
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401
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="plaintext"> "ExecuteTime": {</span>
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439
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<pre style="margin: 0;">-<span id="LC439" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:12:21.993568</span>Z",</span>
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440
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<pre style="margin: 0;">-<span id="LC440" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:12:14.582649</span>Z"</span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:15:58.130952</span>Z",</span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:51.882778</span>Z"</span>
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441
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="plaintext"> },</span>
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442
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="plaintext"> "scrolled": false</span>
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443
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="plaintext"> },</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="452" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -489,11 +452,11 @@</td>
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489
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452
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="plaintext"> },</span>
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490
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453
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<pre style="margin: 0;"> <span id="LC453" class="line" lang="plaintext"> {</span>
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491
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="plaintext"> "cell_type": "code",</span>
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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">10</span>,</span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext"> "execution_count": <span class="idiff left right">7</span>,</span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="plaintext"> "metadata": {</span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="plaintext"> "ExecuteTime": {</span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">02-10T14:12:37.852545</span>Z",</span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">02-10T14:12:25.233754</span>Z"</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext"> "end_time": "2020-<span class="idiff left right">12-16T13:16:10.215380</span>Z",</span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext"> "start_time": "2020-<span class="idiff left right">12-16T13:15:58.819352</span>Z"</span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="plaintext"> },</span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="plaintext"> "scrolled": false</span>
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462
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="plaintext"> },</span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#5c9789bd13fad7443f2bdb7fbf28b9e3b3086ce7"><strong>docs/pycoQC/results/Albacore-1.2.1_basecall-1D-DNA.html</strong></a>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#cb6bc19a259bc5761c431e240df8083f0da43260"><strong>docs/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.html</strong></a>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#054d72dc3e444c540d13876eb45c4b633a1dee0b"><strong>docs/pycoQC/results/Guppy-2.1.3_basecall-1D_RNA.json</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="json"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"pycoqc"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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3
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.5.0.<span class="idiff left right">19</span>"</span><span class="p">,</span></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"date"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1<span class="idiff left right">0/0</span>2/20"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.5.0.<span class="idiff left right">23</span>"</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"date"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1<span class="idiff left right">6/1</span>2/20"</span></span>
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5
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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6
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"All Reads"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"run"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#15447aba8b535818f5798fdc0f72b9791bc6f641"><strong>docs/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.html</strong></a>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#50849afd4e4170b36b4b962754237c3c246f8519"><strong>docs/pycoQC/results/Guppy-2.3_basecall-1D_alignment-DNA.json</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="json"><span class="p">{</span></span>
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2
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"pycoqc"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.5.0.<span class="idiff left right">19</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"date"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1<span class="idiff left right">0/0</span>2/20"</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"2.5.0.<span class="idiff left right">23</span>"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"date"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1<span class="idiff left right">6/1</span>2/20"</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"All Reads"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="json"><span class="w" style="color: #bbb;"> </span><span class="nl">"run"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#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.<span class="idiff left right">0.23</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.<span class="idiff left right">2</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="diff-line-num unfold js-unfold old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,15 +23,14 @@ requirements:</td>
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23
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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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24
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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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25
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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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26
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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="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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<pre style="margin: 0;">-<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">plotly=4.1.0</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">jinja2=2.10.1</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">h5py=2.9.0</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tqdm=4.35.0</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pysam=0.15.3</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;">numpy>=1.19</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;">scipy>=1.5</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;">pandas>=1.1</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;">plotly==4.1.0</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">jinja2>=2.10</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">h5py>=3.1</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">tqdm>=4.54</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">pysam>=0.16</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"><span class="na" style="color: #008080;">test</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">imports</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">@@ -44,10 +43,13 @@ test:</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">Barcode_split --help</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml"></span>
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46
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml"><span class="na" style="color: #008080;">about</span><span class="pi">:</span></span>
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47
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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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48
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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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49
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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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50
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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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51
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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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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">home</span><span class="pi">:</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="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">doc_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://adrienleger.com/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="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;">licence_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://www.gnu.org/licenses/gpl-3.0.en.html</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">summary</span><span class="pi">:</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="LC51" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"><span class="na" style="color: #008080;">extra</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"> <span class="na" style="color: #008080;">author</span><span class="pi">:</span> <span class="s" style="color: #d14;">Adrien Leger & Tommaso Leonardi</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="na" style="color: #008080;">author_email</span><span class="pi">:</span> <span class="s" style="color: #d14;">aleg@ebi.ac.uk</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">author_url</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://adrienleger.com</span></span></pre>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#e06ae62d2bf20523432731a2d6fa671c79156f34"><strong>mkdocs.yml</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Required python packages to generate the documentation</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># * mkdocs</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># * mkdocs-material</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># * pygments</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># * pymdown-extensions</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># * mknotebooks</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Project information</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">site_name</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff right">pycoQC'</span></span></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">site_description</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff">PycoQC</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">computes</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">metrics</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">and</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">generates</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">interactive</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">QC</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">plots</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">for</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Oxford</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Nanopore</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">technologies</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">sequencing</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">data'</span></span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="na" style="color: #008080;">site_author</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff">Adrien</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Leger</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">&</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Tommaso</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">Leonardi'</span></span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">site_url</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff right">https://a-slide.github.io/pycoQC/'</span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">site_name</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">pycoQC</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">site_description</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data</span></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">site_author</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">Adrien Leger & Tommaso Leonardi</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">site_url</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">https://adrienleger.com/pycoQC</span></span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Repository</span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">repo_name</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">a-slide/pycoQC'</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"><span class="na" style="color: #008080;">repo_url</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff right">https://github.com/a-slide/pycoQC'</span></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"><span class="na" style="color: #008080;">repo_url</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">https://github.com/a-slide/pycoQC</span></span></span>
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Copyright</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">copyright</span><span class="pi">:</span> <span class="s1" style="color: #d14;"><span class="idiff left">'</span></span><span class="s" style="color: #d14;"><span class="idiff">Copyright</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">©</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">2019</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Adrien</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Leger</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">&</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Tommaso</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff">Leonardi</span></span><span class="nv" style="color: #008080;"><span class="idiff"> </span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">copyright</span><span class="pi">:</span> <span class="s" style="color: #d14;"><span class="idiff left right">Copyright © 2020 Adrien Leger & Tommaso Leonardi</span></span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Navigation menu</span></span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">nav</span><span class="pi">:</span></span>
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<li id="7fb3feaa708d277c081252e8e3fa1635ac2bc2f8">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#7fb3feaa708d277c081252e8e3fa1635ac2bc2f8"><strong>pycoQC/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2.5.0.23'</span></span>
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<pre style="margin: 0;">+<span id="LC3" 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="LC4" 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;">"2.5.2"</span></span>
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<pre style="margin: 0;">+<span id="LC5" 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="LC6" class="line" lang="python"><span class="n" style="color: #333;">__url__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"https://github.com/a-slide/pycoQC"</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="n" style="color: #333;">__licence__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GPLv3"</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Adrien Leger & Tommaso Leonardi"</span></span>
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<pre style="margin: 0;"> <span id="LC9" 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/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#0ab1bcdf84ca9909a6ba485bccfe1e164d4e47ce"><strong>pycoQC/__main__.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -76,6 +76,8 @@ def main_pycoQC (args=None):</td>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> If not provided, looks for it in ~/.pycoQC and ~/.config/pycoQC/config. If it's still not found, falls back to default parameters.</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> The first level keys are the names of the plots to be included.</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> The second level keys are the parameters to pass to each plotting function (default: %(default)s)")"""</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">parser_html</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--skip_coverage_plot"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Skip the coverage plot in HTML report. Useful when using a reference file containing many sequences, i.e. transcriptome (default: %(default)s)"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="n" style="color: #333;">parser_other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument_group</span><span class="p">(</span><span class="s" style="color: #d14;">'Other options'</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"> <span class="n" style="color: #333;">parser_other</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--sample"</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">100000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">textwrap</span><span class="p">.</span><span class="n" style="color: #333;">dedent</span><span class="p">(</span><span class="s" style="color: #d14;">"""If not None a n number of reads will be randomly selected instead of the entire dataset for ploting function</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">@@ -123,6 +125,7 @@ def main_pycoQC (args=None):</td>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"> <span class="n" style="color: #333;">html_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">html_outfile</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"> <span class="n" style="color: #333;">report_title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">report_title</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python"> <span class="n" style="color: #333;">config_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">config_file</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python"> <span class="n" style="color: #333;">skip_coverage_plot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">skip_coverage_plot</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python"> <span class="n" style="color: #333;">template_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">template_file</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python"> <span class="n" style="color: #333;">json_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">json_outfile</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#f89a550431bcf6a8676496142cf570e96c1375e8"><strong>pycoQC/pycoQC.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">@@ -37,6 +37,7 @@ def pycoQC (</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">config_file</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">template_file</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">json_outfile</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">skip_coverage_plot</span><span class="p">:</span><span class="nb" style="color: #0086b3;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">verbose</span><span class="p">:</span><span class="nb" style="color: #0086b3;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">quiet</span><span class="p">:</span><span class="nb" style="color: #0086b3;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,6 +108,7 @@ def pycoQC (</td>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"> <span class="n" style="color: #333;">config_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_arg</span><span class="p">(</span><span class="s" style="color: #d14;">"config_file"</span><span class="p">,</span> <span class="n" style="color: #333;">config_file</span><span class="p">,</span> <span class="n" style="color: #333;">required_type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">allow_none</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"> <span class="n" style="color: #333;">template_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_arg</span><span class="p">(</span><span class="s" style="color: #d14;">"template_file"</span><span class="p">,</span> <span class="n" style="color: #333;">template_file</span><span class="p">,</span> <span class="n" style="color: #333;">required_type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">allow_none</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"> <span class="n" style="color: #333;">json_outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_arg</span><span class="p">(</span><span class="s" style="color: #d14;">"json_outfile"</span><span class="p">,</span> <span class="n" style="color: #333;">json_outfile</span><span class="p">,</span> <span class="n" style="color: #333;">required_type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="n" style="color: #333;">allow_none</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python"> <span class="n" style="color: #333;">skip_coverage_plot</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_arg</span><span class="p">(</span><span class="s" style="color: #d14;">"skip_coverage_plot"</span><span class="p">,</span> <span class="n" style="color: #333;">skip_coverage_plot</span><span class="p">,</span> <span class="n" style="color: #333;">required_type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">bool</span><span class="p">,</span> <span class="n" style="color: #333;">allow_none</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Print debug info</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span><span class="s" style="color: #d14;">"General info"</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -154,7 +156,8 @@ def pycoQC (</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">html_outfile</span><span class="p">,</span></span>
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">config_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config_file</span><span class="p">,</span></span>
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">template_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">template_file</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python"> <span class="n" style="color: #333;">report_title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">report_title</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="python"> <span class="n" style="color: #333;">report_title</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">report_title</span><span class="p">,</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python"> <span class="n" style="color: #333;">skip_coverage_plot</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">skip_coverage_plot</span><span class="p">)</span></span>
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158
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python"></span>
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162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Run json output function</span></span>
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160
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">json_outfile</span><span class="p">:</span></span>
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<li id="9b423df0151ba310a25db1cea19007f698f3b029">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#9b423df0151ba310a25db1cea19007f698f3b029"><strong>pycoQC/pycoQC_report.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">@@ -59,7 +59,8 @@ class pycoQC_report ():</td>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">outfile</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">config_file</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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61
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61
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">template_file</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">report_title</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PycoQC report"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">report_title</span><span class="p">:</span><span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PycoQC report"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">skip_coverage_plot</span><span class="p">:</span><span class="nb" style="color: #0086b3;">bool</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">):</span></span>
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63
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="s" style="color: #d14;">""""""</span></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Generating HTML report"</span><span class="p">)</span></span>
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -72,6 +73,9 @@ class pycoQC_report ():</td>
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72
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"> <span class="n" style="color: #333;">plots</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="n" style="color: #333;">titles</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">method_name</span><span class="p">,</span> <span class="n" style="color: #333;">method_args</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">config_dict</span><span class="p">.</span><span class="n" style="color: #333;">items</span> <span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">skip_coverage_plot</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">method_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"alignment_coverage"</span><span class="p">:</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Skipping method {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">method_name</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Running method {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">method_name</span><span class="p">))</span></span>
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">debug</span> <span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">{} ({})"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">method_name</span><span class="p">,</span> <span class="n" style="color: #333;">method_args</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -96,7 +100,7 @@ class pycoQC_report ():</td>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">titles</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">plot_title</span><span class="p">)</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">E</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">{}<span class="idiff left">"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"{} is not a valid plotting method"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">method_name</span></span><span class="p"><span class="idiff right">)</span>))</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">{}<span class="idiff left"> is not a valid plotting method"</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">method_name</span></span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">{}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">E</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pycoQCError</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">E</span><span class="p">:</span></span>
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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#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">@@ -4,23 +4,20 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"></span>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="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;">"2.5.0.23"</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="LC7" 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="LC8" 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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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">name</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">description</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">version</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'pycoQC'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">description</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'2.5.2'</span></span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">long_description</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">"text/markdown"</span></span><span class="p">,</span></span>
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19
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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">"https://github.com/a-slide/pycoQC"</span></span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="n" style="color: #333;">long_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'text/markdown'</span></span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">url</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;"><span class="idiff left right">'https://github.com/a-slide/pycoQC'</span></span><span class="p">,</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"> <span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Adrien Leger & Tommaso Leonardi'</span><span class="p">,</span></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'aleg@ebi.ac.uk'</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"> <span class="n" style="color: #333;">license</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'GPLv3'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">python_requires</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3.<span class="idiff left right">5</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="n" style="color: #333;">python_requires</span> <span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'>=3.<span class="idiff left right">6</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="n" style="color: #333;">classifiers</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">'Development Status :: 3 - Alpha'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"> <span class="s" style="color: #d14;">'Intended Audience :: Science/Research'</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,17 +25,17 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="s" style="color: #d14;">'License :: OSI Approved :: GNU General Public License v3 (GPLv3)'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"> <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy<span class="idiff left right">==1.17.1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'scipy<span class="idiff left right">==1.3.1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas<span class="idiff left right">==0.25</span>.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="s" style="color: #d14;">'numpy<span class="idiff left right">>=1.19</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="s" style="color: #d14;">'scipy<span class="idiff left right">>=1.5</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="s" style="color: #d14;">'pandas<span class="idiff left right">>=1</span>.1'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="s" style="color: #d14;">'plotly==4.1.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'jinja2<span class="idiff left right">==2.10.1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"> <span class="s" style="color: #d14;">'h5py<span class="idiff left right">==2.9.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="s" style="color: #d14;">'tqdm<span class="idiff left right">==4.35.0</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="s" style="color: #d14;">'pysam<span class="idiff left right">==0.15.3</span>'</span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">name</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;"><span class="idiff left">name</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">name</span></span><span class="p">},</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;"><span class="idiff left right">name</span></span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'templates/*'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="s" style="color: #d14;">'jinja2<span class="idiff left right">>=2.10</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"> <span class="s" style="color: #d14;">'h5py<span class="idiff left right">>=3.1</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="s" style="color: #d14;">'tqdm<span class="idiff left right">>=4.54</span>'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">'pysam<span class="idiff left right">>=0.16</span>'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">packages</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;"><span class="idiff left right">'pycoQC'</span></span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">package_dir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;"><span class="idiff left">'pycoQC'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'pycoQC'</span></span><span class="p">},</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">package_data</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;"><span class="idiff left right">'pycoQC'</span></span><span class="p">:</span> <span class="p">[</span><span class="s" style="color: #d14;">'templates/*'</span><span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="s" style="color: #d14;">'console_scripts'</span><span class="p">:</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"> <span class="s" style="color: #d14;">'pycoQC=pycoQC.__main__:main_pycoQC'</span><span class="p">,</span></span>
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<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#01bfd3023a57e8ab14b0c062ff9f5e9dab1d45ea"><strong>versipy.yaml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"> <span class="na" style="color: #008080;">major</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"> <span class="na" style="color: #008080;">minor</span><span class="pi">:</span> <span class="m" style="color: #099;">5</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">micro</span><span class="pi">:</span> <span class="m" style="color: #099;">2</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">a</span><span class="pi">:</span> <span class="no" style="color: #008080;">null</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">b</span><span class="pi">:</span> <span class="no" style="color: #008080;">null</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">rc</span><span class="pi">:</span> <span class="no" style="color: #008080;">null</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">post</span><span class="pi">:</span> <span class="no" style="color: #008080;">null</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">dev</span><span class="pi">:</span> <span class="no" style="color: #008080;">null</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">managed_values</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_name__</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_description__</span><span class="pi">:</span> <span class="s" style="color: #d14;">PycoQC computes metrics and generates interactive QC plots</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="s" style="color: #d14;">for Oxford Nanopore technologies sequencing data</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_introduction__</span><span class="pi">:</span> <span class="s" style="color: #d14;">PycoQC relies on the *sequencing_summary.txt* file generated</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"> <span class="s" style="color: #d14;">by Albacore and Guppy, but if needed it can also generate a summary file from</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="s" style="color: #d14;">basecalled fast5 files. The package supports 1D and 1D2 runs generated with Minion,</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="s" style="color: #d14;">Gridion and Promethion devices, basecalled with Albacore 1.2.1+ or Guppy 2.1.3+.</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="s" style="color: #d14;">PycoQC is written in pure Python3. **Python 2 is not supported**. For a quick</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="s" style="color: #d14;">introduction see tutorial by [Tim Kahlke](https://github.com/timkahlke) available</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="s" style="color: #d14;">at https://timkahlke.github.io/LongRead_tutorials/QC_P.html</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_url__</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://github.com/a-slide/pycoQC</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_doc_url__</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://adrienleger.com/pycoQC</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">__author_name__</span><span class="pi">:</span> <span class="s" style="color: #d14;">Adrien Leger & Tommaso Leonardi</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">__author_email__</span><span class="pi">:</span> <span class="s" style="color: #d14;">aleg@ebi.ac.uk</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="na" style="color: #008080;">__author_url__</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://adrienleger.com</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_licence__</span><span class="pi">:</span> <span class="s" style="color: #d14;">GPLv3</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="na" style="color: #008080;">__package_licence_url__</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://www.gnu.org/licenses/gpl-3.0.en.html</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="na" style="color: #008080;">__minimal_python__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">>=3.6'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="na" style="color: #008080;">__entry_point_1__</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC=pycoQC.__main__:main_pycoQC</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">__entry_point_2__</span><span class="pi">:</span> <span class="s" style="color: #d14;">Fast5_to_seq_summary=pycoQC.__main__:main_Fast5_to_seq_summary</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">__entry_point_3__</span><span class="pi">:</span> <span class="s" style="color: #d14;">Barcode_split=pycoQC.__main__:main_Barcode_split</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_1__</span><span class="pi">:</span> <span class="s" style="color: #d14;">numpy>=1.19</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_2__</span><span class="pi">:</span> <span class="s" style="color: #d14;">scipy>=1.5</span></span>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_3__</span><span class="pi">:</span> <span class="s" style="color: #d14;">pandas>=1.1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_4__</span><span class="pi">:</span> <span class="s" style="color: #d14;">plotly==4.1.0</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_5__</span><span class="pi">:</span> <span class="s" style="color: #d14;">jinja2>=2.10</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_6__</span><span class="pi">:</span> <span class="s" style="color: #d14;">h5py>=3.1</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_7__</span><span class="pi">:</span> <span class="s" style="color: #d14;">tqdm>=4.54</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"> <span class="na" style="color: #008080;">__dependency_8__</span><span class="pi">:</span> <span class="s" style="color: #d14;">pysam>=0.16</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="na" style="color: #008080;">__classifiers_1__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Development</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Status</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Alpha'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">__classifiers_2__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Intended</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Audience</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Science/Research'</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">__classifiers_3__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Topic</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Scientific/Engineering</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Bio-Informatics'</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="na" style="color: #008080;">__classifiers_4__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">License</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">OSI</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Approved</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </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;">License</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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">__classifiers_5__</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">Programming</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Language</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">Python</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">::</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">3'</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"><span class="na" style="color: #008080;">managed_files</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/setup.py</span><span class="pi">:</span> <span class="s" style="color: #d14;">setup.py</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/meta.yaml</span><span class="pi">:</span> <span class="s" style="color: #d14;">meta.yaml</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/__init__.py</span><span class="pi">:</span> <span class="s" style="color: #d14;">pycoQC/__init__.py</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/README.md</span><span class="pi">:</span> <span class="s" style="color: #d14;">README.md</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/mkdocs.yml</span><span class="pi">:</span> <span class="s" style="color: #d14;">mkdocs.yml</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="s" style="color: #d14;">.versipy/index.md</span><span class="pi">:</span> <span class="s" style="color: #d14;">docs/index.md</span></span></pre>
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<li id="0a7da04fa26829b6b4004d78e4e945cdec068d7e">
<a href="https://salsa.debian.org/med-team/pycoqc/-/commit/b46d0d7f9e2cd0404101d2c4bbd65df2fa933d43#0a7da04fa26829b6b4004d78e4e945cdec068d7e"><strong>versipy_history.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">2020-12-16 15:55:07.158731 0.0.0 Initialise versipy history</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">2020-12-16 16:35:49.487662 2.5.1.dev1 Versipy auto bump-up</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">2020-12-16 16:37:21.197197 2.5.1.dev2 Versipy auto bump-up</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">2020-12-16 16:38:01.948310 2.5.1.dev3 Versipy auto bump-up</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">2020-12-16 16:40:09.668703 2.5.1.dev4 Versipy auto bump-up</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">2020-12-16 16:41:15.013385 2.5.1.dev5 Versipy auto bump-up</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2020-12-16 16:50:47.571875 2.5.1.dev6 Versipyify package and expose skip_coverage_plot option to CLI</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">2020-12-16 16:58:52.524915 2.5.2 Versipyify package and expose skip_coverage_plot option to CLI</span></pre>
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