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GitLab

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<h3>

Nilesh Patra pushed to branch master

at <a href="https://salsa.debian.org/med-team/python-nanoget">Debian Med / python-nanoget</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-nanoget/-/commit/803c8e5fd35ee3b501395430d078fb5a6369f58b">803c8e5f</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-11-02T03:00:52+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.16.1</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-nanoget/-/commit/ce579a126c4b25bc5270f38e9c07deb725d1024e">ce579a12</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-11-02T03:00:52+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.16.1'

Update to upstream version '1.16.1'

with Debian dir 873858bf6aa8b921c86ff2b2e2d3c8943baf06c6</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/python-nanoget/-/commit/bf5011c7eda06738c1975c8ffcec53cfaac47bd9">bf5011c7</a></strong>

<div>

<span>by Nilesh Patra</span>

<i>at 2021-11-02T03:01:27+05:30</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>9 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

<span class="deleted-file">

−

.travis.yml

</span>

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#f7981066bb546fd6c003f834144546038e06f5c7">

nanoget/extraction_functions.py

</a>

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<li class="file-stats">

<a href="#a1bdc9e8db5c382971f01299733c4620d084d8be">

nanoget/nanoget.py

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<li class="file-stats">

<a href="#fa058a21cf6bef14332b56816c079db58629512c">

nanoget/utils.py

</a>

</li>

<li class="file-stats">

<a href="#9259555c2946f76d9d4444e16669673eba2fdcd9">

nanoget/version.py

</a>

</li>

<li class="file-stats">

<a href="#76292b96a69d28272be547f0f9a608b658bf73ee">

<span class="new-file">

+

scripts/create_feather.py

</span>

</a>

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<li class="file-stats">

<a href="#3e37c6bf1fb9daa65897d3d75f698e0771c8a42e">

scripts/test.py

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong>

deleted

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">cp README.md README.rst</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install flake8</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">pip install -e .</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bash scripts/test.sh</span></span>

</pre>

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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;">flake8 nanoget/nanoget.py</span></span>

</pre>

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18

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"></span>

</pre>

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19

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">notifications</span><span class="pi">:</span></span>

</pre>

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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;">email</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="21" 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">

21

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">  <span class="na" style="color: #008080;">webhooks</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" 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">

22

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">    <span class="na" style="color: #008080;">urls</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="23" 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">

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;">https://webhooks.gitter.im/e/4b1c45cea6826ce475c2</span></span></pre>

</td>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-nanoget (1.16.1-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * New upstream version 1.16.1</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" 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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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Nilesh Patra <nilesh@debian.org>  Tue, 02 Nov 2021 03:01:08 +0530</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>

</pre>

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1

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">python-nanoget (1.12.2-5) unstable; urgency=medium</span>

</pre>

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2

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" 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">

3

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<td class="new_line diff-line-num" data-linenumber="10" 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">

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">  * Team Upload.</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f7981066bb546fd6c003f834144546038e06f5c7">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#f7981066bb546fd6c003f834144546038e06f5c7"><strong>nanoget/extraction_functions.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,10 +4,10 @@ import nanoget.utils as ut</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">nanomath</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">concurrent.futures</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">cfutures</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">itertools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">repeat</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">process_summary</span><span class="p">(</span><span class="n" style="color: #333;">summaryfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" 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">@@ -128,7 +128,7 @@ def process_ubam(bam, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">        <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">AlignmentFile</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">,</span> <span class="n" style="color: #333;">check_sq</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="LC129" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: No index for bam file could be found, created index."</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;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python">        <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">nanomath</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">),</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="131" 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="LC131" class="line" lang="python">        <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">ut</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">),</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">              <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">until_eof</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">])</span> \</span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">        <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</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">@@ -154,20 +154,29 @@ def process_bam(bam, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: Starting to collect statistics from bam file {}."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">    <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_bam</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">    <span class="n" style="color: #333;">chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">references</span></span>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)]</span></span>

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: lots of contigs (>100), not running in separate processes"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="python">        <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">([</span><span class="n" style="color: #333;">bam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">),</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">cfutures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">max_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"threads"</span><span class="p">])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">executor</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC157" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"huge"</span><span class="p">]:</span></span>

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<pre style="margin: 0;">+<span id="LC158" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: lots of contigs (>100) or --huge, not running in separate processes"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">        <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sublist</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">executor</span></span><span class="p"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">extract_from_bam</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">params</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">res</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sublist</span></span><span class="p"><span class="idiff right">]</span>,</span></span>

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<pre style="margin: 0;">+<span id="LC160" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">extract_from_bam</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">bam</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kwargs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"keep_supp"</span></span><span class="p"><span class="idiff right">])</span>,</span></span>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">            <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"aligned_quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">                     <span class="s" style="color: #d14;">"aligned_lengths"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mapQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"percentIdentity"</span><span class="p">])</span> \</span>

</pre>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">            <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</span><span class="p">)</span> \</span>

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<td class="new_line diff-line-num" data-linenumber="164" 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="LC164" class="line" lang="python">            <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'any'</span><span class="p">)</span></span>

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<td class="new_line diff-line-num old" data-linenumber="165" 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="LC169" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: bam {} contains {} primary alignments."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python">        <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">datadf</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="165" 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="LC165" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC166" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python">        <span class="n" style="color: #333;">unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chromosomes</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="168" 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="LC168" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">cfutures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">max_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"threads"</span><span class="p">])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">executor</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="169" 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="LC169" class="line" lang="python">            <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="170" 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="LC170" class="line" lang="python">                <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">res</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sublist</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">extract_from_bam</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python">                                                      <span class="n" style="color: #333;">repeat</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="172" 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="LC172" class="line" lang="python">                                                      <span class="n" style="color: #333;">unit</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python">                                                      <span class="n" style="color: #333;">repeat</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"keep_supp"</span><span class="p">]))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="174" 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="LC174" class="line" lang="python">                      <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sublist</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python">                <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"aligned_quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">                         <span class="s" style="color: #d14;">"aligned_lengths"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mapQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"percentIdentity"</span><span class="p">])</span> \</span>

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">                <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</span><span class="p">)</span> \</span>

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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python">                <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'any'</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Nanoget: bam </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">bam</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> contains </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">datadf</span><span class="p">[</span><span class="s" style="color: #d14;">'lengths'</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> primary alignments."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">reduce_memory_usage</span><span class="p">(</span><span class="n" style="color: #333;">datadf</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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">@@ -187,20 +196,25 @@ def process_cram(cram, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: Starting to collect statistics from cram file {}."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">cram</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">    <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">check_bam</span><span class="p">(</span><span class="n" style="color: #333;">cram</span><span class="p">,</span> <span class="n" style="color: #333;">samtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"cram"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">    <span class="n" style="color: #333;">chromosomes</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">references</span></span>

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<td class="new_line diff-line-num old" data-linenumber="199" 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="LC190" class="line" lang="python">    <span class="n" style="color: #333;">params</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">([</span><span class="n" style="color: #333;">cram</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">),</span> <span class="n" style="color: #333;">chromosomes</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="199" 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="LC199" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">chromosomes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">100</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="200" 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="LC200" class="line" lang="python">        <span class="n" style="color: #333;">unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="bp" style="color: #999;">None</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="201" 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="LC201" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: lots of contigs (>100), not running in separate processes"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="202" 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="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num new" data-linenumber="203" 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="LC203" class="line" lang="python">        <span class="n" style="color: #333;">unit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">chromosomes</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="191" 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="new_line diff-line-num" data-linenumber="204" 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="LC204" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">cfutures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">max_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"threads"</span><span class="p">])</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">executor</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="192" 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="new_line diff-line-num" data-linenumber="205" 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="LC205" class="line" lang="python">        <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pd</span><span class="p">.</span><span class="n" style="color: #333;">DataFrame</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="206" 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="LC193" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">res</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sublist</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">extract_from_bam</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sublist</span><span class="p">],</span></span>

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<td class="old_line diff-line-num new" data-linenumber="194" 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="new_line diff-line-num new" data-linenumber="206" 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="LC206" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">res</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sublist</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">extract_from_bam</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="194" 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="new_line diff-line-num new" data-linenumber="207" 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="LC207" class="line" lang="python">                                                  <span class="n" style="color: #333;">repeat</span><span class="p">(</span><span class="n" style="color: #333;">cram</span><span class="p">),</span> <span class="n" style="color: #333;">unit</span><span class="p">,</span> <span class="n" style="color: #333;">repeat</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">[</span><span class="s" style="color: #d14;">"keep_supp"</span><span class="p">]))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="208" 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="LC208" class="line" lang="python">                  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">res</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sublist</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">            <span class="n" style="color: #333;">columns</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"readIDs"</span><span class="p">,</span> <span class="s" style="color: #d14;">"quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"aligned_quals"</span><span class="p">,</span> <span class="s" style="color: #d14;">"lengths"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python">                     <span class="s" style="color: #d14;">"aligned_lengths"</span><span class="p">,</span> <span class="s" style="color: #d14;">"mapQ"</span><span class="p">,</span> <span class="s" style="color: #d14;">"percentIdentity"</span><span class="p">])</span> \</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python">            <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'columns'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'all'</span><span class="p">)</span> \</span>

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<td class="new_line diff-line-num" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python">            <span class="p">.</span><span class="n" style="color: #333;">dropna</span><span class="p">(</span><span class="n" style="color: #333;">axis</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="n" style="color: #333;">how</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'any'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="213" 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="LC198" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: cram {} contains {} primary alignments."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" 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="new_line diff-line-num old" data-linenumber="213" 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="LC199" class="line" lang="python">        <span class="n" style="color: #333;">cram</span><span class="p">,</span> <span class="n" style="color: #333;">datadf</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths"</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">))</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="200" 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="new_line diff-line-num new" data-linenumber="213" 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="LC213" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="sa">f</span><span class="s" style="color: #d14;">"Nanoget: cram </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">cram</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> contains </span><span class="si" style="color: #d14;">{</span><span class="n" style="color: #333;">datadf</span><span class="p">[</span><span class="s" style="color: #d14;">'lengths'</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="si" style="color: #d14;">}</span><span class="s" style="color: #d14;"> primary alignments."</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="214" 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="LC214" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">reduce_memory_usage</span><span class="p">(</span><span class="n" style="color: #333;">datadf</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_from_bam</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">params</span></span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">extract_from_bam</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">bam</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">chromosome</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">keep_supplementary</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">    <span class="s" style="color: #d14;">"""Extracts metrics from bam.</span></span>

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="python"><span class="s" style="color: #d14;">    Worker function per chromosome</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">@@ -212,18 +226,29 @@ def extract_from_bam(params):</td>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python"><span class="s" style="color: #d14;">    -mapping qualities</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python"><span class="s" style="color: #d14;">    -edit distances to the reference genome scaled by read length</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">    <span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">chromosome</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">params</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">    <span class="n" style="color: #333;">samfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">AlignmentFile</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="s" style="color: #d14;">"rb"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">        <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="230" 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="LC219" class="line" lang="python">         <span class="n" style="color: #333;">nanomath</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="python">         <span class="n" style="color: #333;">nanomath</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_qualities</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">         <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="python">         <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="python">         <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">mapping_quality</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="python">         <span class="n" style="color: #333;">get_pID</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="n" style="color: #333;">multiple_iterators</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_secondary</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_unmapped</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keep_supplementary</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC231" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="232" 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="LC232" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="227" 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="new_line diff-line-num new" data-linenumber="233" 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="LC233" class="line" lang="python">             <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="234" 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="LC234" class="line" lang="python">             <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_qualities</span><span class="p">),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="235" 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="LC235" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="227" 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="new_line diff-line-num new" data-linenumber="236" 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="LC236" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="227" 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="new_line diff-line-num new" data-linenumber="237" 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="LC237" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">mapping_quality</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="227" 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="new_line diff-line-num new" data-linenumber="238" 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="LC238" class="line" lang="python">             <span class="n" style="color: #333;">get_pID</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="239" 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="LC239" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="n" style="color: #333;">multiple_iterators</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="240" 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="LC240" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_secondary</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_unmapped</span><span class="p">]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="241" 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="LC241" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="242" 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="LC242" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="243" 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="LC243" class="line" lang="python">            <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_name</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC244" class="line" lang="python">             <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_qualities</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python">             <span class="n" style="color: #333;">ut</span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_qualities</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC246" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_length</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">query_alignment_length</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python">             <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">mapping_quality</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python">             <span class="n" style="color: #333;">get_pID</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="LC250" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">samfile</span><span class="p">.</span><span class="n" style="color: #333;">fetch</span><span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">chromosome</span><span class="p">,</span> <span class="n" style="color: #333;">multiple_iterators</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="LC251" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_secondary</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_unmapped</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">read</span><span class="p">.</span><span class="n" style="color: #333;">is_supplementary</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_pID</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="310" 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">@@ -310,7 +335,7 @@ def extract_from_fastq(fq):</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python"><span class="s" style="color: #d14;">    Return average quality and read length</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">rec</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SeqIO</span><span class="p">.</span><span class="n" style="color: #333;">parse</span><span class="p">(</span><span class="n" style="color: #333;">fq</span><span class="p">,</span> <span class="s" style="color: #d14;">"fastq"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;"><span class="idiff left right">nanomath</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python">        <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;"><span class="idiff left right">ut</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC340" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">stream_fastq_full</span><span class="p">(</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="336" 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="361" 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">@@ -336,8 +361,8 @@ def extract_all_from_fastq(rec):</td>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="nb" style="color: #0086b3;">id</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python">            <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">nanomath</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span></span>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left">nanomath</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">median_qual</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">rec</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">letter_annotations</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"phred_quality"</span></span><span class="p"><span class="idiff right">])</span>)</span></span>

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<pre style="margin: 0;">+<span id="LC364" class="line" lang="python">            <span class="n" style="color: #333;"><span class="idiff left right">ut</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span></span>

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<pre style="margin: 0;">+<span id="LC365" class="line" lang="python">            <span class="bp" style="color: #999;"><span class="idiff left right">None</span></span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">info_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">info</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="364" 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="389" 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">@@ -364,7 +389,7 @@ def process_fastq_rich(fastq, **kwargs):</td>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python">        <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">            <span class="n" style="color: #333;">read_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">info_to_dict</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">description</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">            <span class="n" style="color: #333;">res</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC367" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">nanomath</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span></span>

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<pre style="margin: 0;">+<span id="LC392" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">ut</span></span><span class="p">.</span><span class="n" style="color: #333;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">letter_annotations</span><span class="p">[</span><span class="s" style="color: #d14;">"phred_quality"</span><span class="p">]),</span></span>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">                 <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">                 <span class="n" style="color: #333;">read_info</span><span class="p">[</span><span class="s" style="color: #d14;">"ch"</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC395" class="line" lang="python">                 <span class="n" style="color: #333;">read_info</span><span class="p">[</span><span class="s" style="color: #d14;">"start_time"</span><span class="p">],</span></span>

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<br>

</li>

<li id="a1bdc9e8db5c382971f01299733c4620d084d8be">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#a1bdc9e8db5c382971f01299733c4620d084d8be"><strong>nanoget/nanoget.py</strong></a>

<hr>

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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">@@ -27,7 +27,7 @@ import nanoget.extraction_functions as ex</td>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_input</span><span class="p">(</span><span class="n" style="color: #333;">source</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">readtype</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1D"</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">              <span class="n" style="color: #333;">combine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"simple"</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">barcoded</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;">huge</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="LC30" class="line" lang="python">              <span class="n" style="color: #333;">combine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"simple"</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">barcoded</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;">huge</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">keep_supp</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff right">True</span></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;">"""Get input and process accordingly.</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">    Data can be:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="79" 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">@@ -79,13 +79,17 @@ def get_input(source, files, threads=4, readtype="1D",</td>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">        <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">proc_functions</span><span class="p">[</span><span class="n" style="color: #333;">source</span><span class="p">](</span><span class="n" style="color: #333;">files</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">                                        <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threadsleft</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;">readtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readtype</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;">barcoded</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">barcoded</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;">barcoded</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">barcoded</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;">keep_supp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">keep_supp</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">                                        <span class="n" style="color: #333;">huge</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="LC85" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">        <span class="k" style="font-weight: 600;">with</span> <span class="n" style="color: #333;">cfutures</span><span class="p">.</span><span class="n" style="color: #333;">ProcessPoolExecutor</span><span class="p">(</span><span class="n" style="color: #333;">max_workers</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">filethreads</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">executor</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">            <span class="n" style="color: #333;">extraction_function</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">proc_functions</span><span class="p">[</span><span class="n" style="color: #333;">source</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">                                          <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">threadsleft</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">                                          <span class="n" style="color: #333;">readtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">readtype</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="python">                                          <span class="n" style="color: #333;">barcoded</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">barcoded</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">                                          <span class="n" style="color: #333;">barcoded</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">barcoded</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python">                                          <span class="n" style="color: #333;">keep_supp</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">keep_supp</span><span class="p">,</span></span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">                                          <span class="n" style="color: #333;">huge</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="LC93" class="line" lang="python">            <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">combine_dfs</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">                <span class="n" style="color: #333;">dfs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">out</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">out</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">executor</span><span class="p">.</span><span class="nb" style="color: #0086b3;">map</span><span class="p">(</span><span class="n" style="color: #333;">extraction_function</span><span class="p">,</span> <span class="n" style="color: #333;">files</span><span class="p">)],</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python">                <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">files</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -95,13 +99,13 @@ def get_input(source, files, threads=4, readtype="1D",</td>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python">    <span class="n" style="color: #333;">datadf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">calculate_start_time</span><span class="p">(</span><span class="n" style="color: #333;">datadf</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python">    <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: Gathered all metrics of {} reads"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">datadf</span><span class="p">)))</span></span>

</pre>

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97

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">datadf</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="102" 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="LC98" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: no reads retrieved."</span><span class="p"><span class="idiff left">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">datadf</span></span><span class="p"><span class="idiff right">))</span>)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="102" 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="LC102" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">critical</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: no reads retrieved."</span><span class="p">)</span></span>

</pre>

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99

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<td class="new_line diff-line-num" data-linenumber="103" 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">

103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"Fatal: No reads found in input."</span><span class="p">)</span></span>

</pre>

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100

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="101" 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="LC105" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">datadf</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="102" 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">

102

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<td class="new_line diff-line-num" data-linenumber="106" 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="LC106" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="108" 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="LC104" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">combine_dfs</span><span class="p">(</span><span class="n" style="color: #333;">dfs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">combine_dfs</span><span class="p">(</span><span class="n" style="color: #333;">dfs</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p">,</span> <span class="n" style="color: #333;">method</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'simple'</span></span><span class="p">):</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">    <span class="s" style="color: #d14;">"""Combine dataframes.</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="106" 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="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="107" 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="new_line diff-line-num" data-linenumber="111" 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="LC111" class="line" lang="python"><span class="s" style="color: #d14;">    Combination is either done simple by just concatenating the DataFrames</span></span>

</pre>

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<br>

</li>

<li id="fa058a21cf6bef14332b56816c079db58629512c">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#fa058a21cf6bef14332b56816c079db58629512c"><strong>nanoget/utils.py</strong></a>

<hr>

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<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">@@ -2,6 +2,7 @@ import sys</td>

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<td class="new_line diff-line-num" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">logging</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

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<td class="new_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">os</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">path</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">opath</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">math</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">log</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">reduce_memory_usage</span><span class="p">(</span><span class="n" style="color: #333;">df</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="33" 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">@@ -32,3 +33,26 @@ def check_existance(f):</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">opath</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"Nanoget: File provided doesn't exist or the path is incorrect: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">"File provided doesn't exist or the path is incorrect: {}"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">errs_tab</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="p">):</span></span>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">    <span class="s" style="color: #d14;">"""Generate list of error rates for qualities less than equal than n."""</span></span>

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<td class="new_line diff-line-num new" data-linenumber="40" 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="LC40" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="o" style="font-weight: 600;">**</span><span class="p">(</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">/</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)]</span></span>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">ave_qual</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">qround</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;">tab</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">errs_tab</span><span class="p">(</span><span class="mi" style="color: #099;">128</span><span class="p">)):</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="44" 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="LC44" class="line" lang="python">    <span class="s" style="color: #d14;">"""Calculate average basecall quality of a read.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;">    Receive the integer quality scores of a read and return the average quality for that read</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="47" 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="LC47" class="line" lang="python"><span class="s" style="color: #d14;">    First convert Phred scores to probabilities,</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="s" style="color: #d14;">    calculate average error probability</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="49" 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="LC49" class="line" lang="python"><span class="s" style="color: #d14;">    convert average back to Phred scale</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">quals</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">        <span class="n" style="color: #333;">mq</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">10</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">log</span><span class="p">(</span><span class="nb" style="color: #0086b3;">sum</span><span class="p">([</span><span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">q</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">q</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">quals</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">),</span> <span class="mi" style="color: #099;">10</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qround</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" 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">

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<td class="new_line diff-line-num new" data-linenumber="54" 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="LC54" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">mq</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mq</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" 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="LC58" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span></pre>

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</table>

<br>

</li>

<li id="9259555c2946f76d9d4444e16669673eba2fdcd9">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#9259555c2946f76d9d4444e16669673eba2fdcd9"><strong>nanoget/version.py</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" 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;">"1.1<span class="idiff left right">2.2</span>"</span></span></pre>

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<pre style="margin: 0;">+<span id="LC1" 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;">"1.1<span class="idiff left right">6.1</span>"</span></span></pre>

</td>

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</table>

<br>

</li>

<li id="76292b96a69d28272be547f0f9a608b658bf73ee">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#76292b96a69d28272be547f0f9a608b658bf73ee"><strong>scripts/create_feather.py</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># wdecoster</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>

</pre>

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4

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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="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nanoget</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">get_input</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="10" 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">

10

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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="LC10" class="line" lang="python">    <span class="s" style="color: #d14;">'''</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="11" 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">

11

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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="LC11" class="line" lang="python"><span class="s" style="color: #d14;">    Organization function</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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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="LC12" class="line" lang="python"><span class="s" style="color: #d14;">    -setups logging</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="s" style="color: #d14;">    -gets inputdata</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="s" style="color: #d14;">    -calls plotting function</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

15

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="s" style="color: #d14;">    '''</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_args</span><span class="p">()</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">    <span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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">

19

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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="LC19" class="line" lang="python">        <span class="s" style="color: #d14;">"fastq"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastq</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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">

20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python">        <span class="s" style="color: #d14;">"bam"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bam</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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">

21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">        <span class="s" style="color: #d14;">"cram"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">cram</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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">

22

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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="LC22" class="line" lang="python">        <span class="s" style="color: #d14;">"fastq_rich"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastq_rich</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">        <span class="s" style="color: #d14;">"fastq_minimal"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fastq_minimal</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="24" 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="LC24" class="line" lang="python">        <span class="s" style="color: #d14;">"summary"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">summary</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python">        <span class="s" style="color: #d14;">"fasta"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">fasta</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="26" 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">

26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">        <span class="s" style="color: #d14;">"ubam"</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ubam</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python">    <span class="p">}</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="28" 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="LC28" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">force</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Output file {} already exists."</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="31" 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="LC31" class="line" lang="python">        <span class="n" style="color: #333;">get_input</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="32" 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="LC32" class="line" lang="python">            <span class="n" style="color: #333;">source</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">n</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sources</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">s</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="33" 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">

33

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">            <span class="n" style="color: #333;">files</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="n" style="color: #333;">f</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">f</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sources</span><span class="p">.</span><span class="n" style="color: #333;">values</span><span class="p">()</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">f</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">            <span class="n" style="color: #333;">threads</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;">threads</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python">            <span class="n" style="color: #333;">readtype</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;">readtype</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="36" 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="LC36" class="line" lang="python">            <span class="n" style="color: #333;">combine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"simple"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="37" 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="LC37" class="line" lang="python">            <span class="n" style="color: #333;">barcoded</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;">barcoded</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="38" 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">

38

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python">            <span class="n" style="color: #333;">huge</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;">huge</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">            <span class="n" style="color: #333;">keep_supp</span><span class="o" style="font-weight: 600;">=</span><span class="ow" style="font-weight: 600;">not</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">no_supplementary</span><span class="p">))</span> \</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="40" 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="LC40" class="line" lang="python">            <span class="p">.</span><span class="n" style="color: #333;">to_feather</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">output</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_args</span><span class="p">():</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="44" 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="LC44" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="45" 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">

45

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<pre style="margin: 0;">+<span id="LC45" 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;">"Creates various plots for long read sequencing data."</span><span class="p">.</span><span class="n" style="color: #333;">upper</span><span class="p">(),</span></span>

</pre>

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<td class="new_line diff-line-num new" 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="python">        <span class="n" style="color: #333;">add_help</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="47" 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">

47

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">general</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>

</pre>

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<td class="new_line diff-line-num new" 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="python">        <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'General options'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="49" 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">

49

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-h"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--help"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="50" 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">

50

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python">                         <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"help"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="51" 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">

51

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<pre style="margin: 0;">+<span id="LC51" 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;">"show the help and exit"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="52" 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">

52

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--threads"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="53" 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">

53

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<pre style="margin: 0;">+<span id="LC53" 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;">"Set the allowed number of threads to be used by the script"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="54" 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="LC54" class="line" lang="python">                         <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="55" 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">

55

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">                         <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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="56" 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">

56

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--huge"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" 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">

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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="LC57" 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;">"Input data is one very large file."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="58" 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="LC58" class="line" lang="python">                         <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>

</pre>

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<td class="new_line diff-line-num new" 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="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"-o"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--output"</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="60" 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">

60

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<pre style="margin: 0;">+<span id="LC60" 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;">"Specify name of feather file."</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="python">                         <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"NanoPlot-data.feather"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="62" 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">

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--readtype"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">                         <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Which read type to extract information about from summary. </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="64" 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">

64

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="s" style="color: #d14;">                                 Options are 1D, 2D, 1D2"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">                         <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"1D"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">                         <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'1D'</span><span class="p">,</span> <span class="s" style="color: #d14;">'2D'</span><span class="p">,</span> <span class="s" style="color: #d14;">'1D2'</span><span class="p">])</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--barcoded"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="68" 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">

68

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<pre style="margin: 0;">+<span id="LC68" 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;">"Use if you want to split the summary file by barcode"</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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="python">                         <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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="70" 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">

70

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--no_supplementary"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="71" 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">

71

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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="LC71" 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;">"Use if you want to remove supplementary alignments"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="72" 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">

72

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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="LC72" class="line" lang="python">                         <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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" 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="python">                         <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>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="74" 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">

74

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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="LC74" class="line" lang="python">    <span class="n" style="color: #333;">general</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--force"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC75" 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;">"Overwrite existing feather files"</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">                         <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>

</pre>

</td>

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77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">                         <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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="78" 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">

78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">    <span class="n" style="color: #333;">target</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>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" 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">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">        <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Input data sources, one of these is required."</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="80" 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">

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="p">.</span><span class="n" style="color: #333;">add_mutually_exclusive_group</span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="81" 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">

81

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python">        <span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="82" 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">

82

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--fastq"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="83" 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">

83

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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="s" style="color: #d14;">"Data is in one or more default fastq file(s)."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="85" 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">

85

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="86" 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">

86

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--fasta"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="87" 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">

87

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<pre style="margin: 0;">+<span id="LC87" 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;">"Data is in one or more fasta file(s)."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="88" 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">

88

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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="LC88" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="89" 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">

89

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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="90" 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">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--fastq_rich"</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="91" 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">

91

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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="LC91" 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;">"Data is in one or more fastq file(s) generated by albacore, </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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="new_line diff-line-num new" data-linenumber="92" 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">

92

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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="LC92" class="line" lang="python"><span class="s" style="color: #d14;">                               MinKNOW or guppy with additional information </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="93" 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">

93

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"><span class="s" style="color: #d14;">                               concerning channel and time."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="94" 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">

94

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="95" 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">

95

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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="96" 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">

96

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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--fastq_minimal"</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="97" 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">

97

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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="LC97" 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;">"Data is in one or more fastq file(s) generated by albacore, </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="98" 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">

98

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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">                               MinKNOW or guppy with additional information concerning channel </span><span class="se" style="color: #d14;">\</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="99" 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">

99

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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="LC99" class="line" lang="python"><span class="s" style="color: #d14;">                               and time. Is extracted swiftly without elaborate checks."</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="102" 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">

102

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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="LC102" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--summary"</span><span class="p">,</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="103" 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">

103

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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="LC103" 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;">"Data is in one or more summary file(s) generated by albacore </span><span class="se" style="color: #d14;">\</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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="python"><span class="s" style="color: #d14;">                               or guppy."</span><span class="p">,</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" 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">

105

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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="LC105" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" 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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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

107

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--bam"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

108

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC108" 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;">"Data is in one or more sorted bam file(s)."</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

109

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC109" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span></span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

110

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC110" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

111

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--ubam"</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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">

</td>

<td class="new_line diff-line-num new" data-linenumber="112" 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">

112

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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="LC112" 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;">"Data is in one or more unmapped bam file(s)."</span><span class="p">,</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="0" 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="LC113" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</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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<td class="new_line diff-line-num new" data-linenumber="114" 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">

114

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="115" 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">

115

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python">    <span class="n" style="color: #333;">mtarget</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--cram"</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC116" 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;">"Data is in one or more sorted cram file(s)."</span><span class="p">,</span></span>

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<td class="new_line diff-line-num new" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

117

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python">                         <span class="n" style="color: #333;">nargs</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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<td class="new_line diff-line-num new" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python">                         <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"file"</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

119

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

120

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="3e37c6bf1fb9daa65897d3d75f698e0771c8a42e">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#3e37c6bf1fb9daa65897d3d75f698e0771c8a42e"><strong>scripts/test.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,7 @@ import nanoget</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_tests</span><span class="p">():</span></span>

</pre>

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5

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<td class="new_line diff-line-num" 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="python">    <span class="s" style="color: #d14;">"""Test functions using testdata from the nanotest repo."""</span></span>

</pre>

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6

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<td class="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python">    <span class="n" style="color: #333;">nanoget</span><span class="p">.</span><span class="n" style="color: #333;">get_input</span><span class="p">(</span><span class="s" style="color: #d14;">"bam"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"nanotest/alignment.bam"</span><span class="p">])</span></span>

</pre>

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<td class="new_line diff-line-num new" 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;">nanoget</span><span class="p">.</span><span class="n" style="color: #333;">get_input</span><span class="p">(</span><span class="s" style="color: #d14;">"bam"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"nanotest/alignment.bam"</span><span class="p">],</span> <span class="n" style="color: #333;">keep_supp</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">)</span></span>

</pre>

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7

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<td class="new_line diff-line-num" 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">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python">    <span class="n" style="color: #333;">nanoget</span><span class="p">.</span><span class="n" style="color: #333;">get_input</span><span class="p">(</span><span class="s" style="color: #d14;">"fastq_rich"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"nanotest/reads.fastq.gz"</span><span class="p">])</span></span>

</pre>

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8

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">nanoget</span><span class="p">.</span><span class="n" style="color: #333;">get_input</span><span class="p">(</span><span class="s" style="color: #d14;">"summary"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"nanotest/sequencing_summary.txt"</span><span class="p">],</span> <span class="n" style="color: #333;">combine</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"track"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">    <span class="n" style="color: #333;">nanoget</span><span class="p">.</span><span class="n" style="color: #333;">get_input</span><span class="p">(</span><span class="s" style="color: #d14;">"fastq_minimal"</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"nanotest/reads.fastq.gz"</span><span class="p">])</span></span>

</pre>

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<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/python-nanoget/-/compare/0afac56a7b789f4d7c9e90474f573be83d86a383...bf5011c7eda06738c1975c8ffcec53cfaac47bd9#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,12 +19,12 @@ setup(</td>

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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;">'https://github.com/wdecoster/nanoget'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">    <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Wouter De Coster'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="21" 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="new_line diff-line-num" data-linenumber="21" 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="LC21" 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;">'decosterwouter@gmail.com'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="22" 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="new_line diff-line-num old" data-linenumber="22" 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="LC22" 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;">'<span class="idiff left right">MIT</span>'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num new" 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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<td class="new_line diff-line-num new" 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="python">    <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left right">GPLv3</span>'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC23" 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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="24" 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="new_line diff-line-num" data-linenumber="24" 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="LC24" class="line" lang="python">        <span class="s" style="color: #d14;">'Development Status :: 4 - Beta'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="25" 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="new_line diff-line-num" data-linenumber="25" 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="LC25" class="line" lang="python">        <span class="s" style="color: #d14;">'Intended Audience :: Science/Research'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="26" 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="new_line diff-line-num" data-linenumber="26" 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="LC26" class="line" lang="python">        <span class="s" style="color: #d14;">'Topic :: Scientific/Engineering :: Bio-Informatics'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="27" 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="new_line diff-line-num old" data-linenumber="27" 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="LC27" class="line" lang="python">        <span class="s" style="color: #d14;">'License :: OSI Approved :: <span class="idiff left right">MIT License</span>'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="28" 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="new_line diff-line-num new" 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">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="s" style="color: #d14;">'License :: OSI Approved :: <span class="idiff left right">GNU General Public License v3 (GPLv3)</span>'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" 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="LC28" class="line" lang="python">        <span class="s" style="color: #d14;">'Programming Language :: Python :: 3'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="29" 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="new_line diff-line-num" data-linenumber="29" 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="LC29" class="line" lang="python">        <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.3'</span><span class="p">,</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="30" 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="new_line diff-line-num" data-linenumber="30" 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="LC30" class="line" lang="python">        <span class="s" style="color: #d14;">'Programming Language :: Python :: 3.4'</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="36" 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="36" 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">@@ -36,7 +36,6 @@ setup(</td>

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<td class="old_line diff-line-num" data-linenumber="36" 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="LC36" 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 class="s" style="color: #d14;">'pandas>=0.22.0'</span><span class="p">,</span></span>

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<td class="old_line diff-line-num" data-linenumber="37" 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="new_line diff-line-num" data-linenumber="37" 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="LC37" class="line" lang="python">                      <span class="s" style="color: #d14;">'numpy'</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;">'biopython'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python">                      <span class="s" style="color: #d14;">'pysam>0.10.0.0'</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;">'nanomath'</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">                      <span class="s" style="color: #d14;">'pysam>0.10.0.0'</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="s" style="color: #d14;">'nanoget'</span><span class="p">:</span> <span class="s" style="color: #d14;">'nanoget'</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;">data_files</span><span class="o" style="font-weight: 600;">=</span><span class="p">[(</span><span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">"LICENSE"</span><span class="p">])])</span></span></pre>

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