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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/scrappie">Debian Med / scrappie</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/scrappie/-/commit/201d05288946b88019d2d417135daab21674377a">201d0528</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-25T19:59:11+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scrappie/-/commit/afa9159a5f99a34c8044b173d209321e62ec46ff">afa9159a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-25T14:39:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/scrappie/-/commit/a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a">a973b0d3</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-10-25T20:16:43+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
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<h4>7 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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debian/manpages
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debian/scrappie.1
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debian/tests/control
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debian/tests/run-unit-test
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debian/tests/simple_test.py
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">scrappie (1.4.2-3) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Add manpage</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Sun, 25 Oct 2020 20:01:22 +0530</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">scrappie (1.4.2-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Team upload.</span>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"help"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#a0b335eb38cfbaa881765c761d5c4e0700ea9a5c"><strong>debian/scrappie.1</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SCRAPPIE "1" "October 2020" "scrappie 1.4.2" "User Commands"</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">scrappie \- basecaller for Nanopore sequencer</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Scrappie is a technology demonstrator for the Oxford Nanopore Technologies</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Limited Research Algorithms group.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Basic usage:</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* scrappie events Base call from event based data.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">* scrappie help Print general help or help about specific Scrappie command.</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">* scrappie licence Print licensing information.</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">* scrappie raw Base call directly from raw signal.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">* scrappie version Print version information.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">* scrappie squiggle Create approximate squiggle for sequence</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">* scrappie mappy Map signal to approximate squiggle</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">* scrappie seqmappy Map signal to sequence via basecall posteriors</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">* scrappie event_table Output table of events for read</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">This project began life as a proof (bet) that a base caller could be written</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">in a low level language in under 8 hours. Some of the poor and just plain odd</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">design decisions, along with the lack of documentation, are a result of its</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">inception. In keeping with ONT's fish naming policy, the project was originally</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">called Crappie.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Scrappie's purpose is to demonstrate the next generation of base calling and, as</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">such, may change drastically between releases and breaks backwards</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">compatibility. Newer versions may drop support of current features or change their</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">behaviour.</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.SH AUTHOR</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> This manpage was written by Nilesh Patra for the Debian distribution and</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<li id="83223a554d33ba7e1888274ff8ac43adb8147ba0">
<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @, python3</span></pre>
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<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"scrappie"</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">CUR_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="sb" style="color: #d14;">`</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/reads <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">CUR_DIR</span><span class="k" style="font-weight: 600;">}</span>/misc <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test functionality"</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 1"</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">scrappie raw <span class="nt" style="color: #000080;">-f</span> sam reads <span class="nt" style="color: #000080;">--min_prob</span><span class="o" style="font-weight: 600;">=</span>0.1 <span class="nt" style="color: #000080;">--format</span><span class="o" style="font-weight: 600;">=</span>FASTA <span class="nt" style="color: #000080;">--output</span><span class="o" style="font-weight: 600;">=</span>test1.fa</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> test1.fa <span class="o" style="font-weight: 600;">]</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> 1 test1.fa</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 2"</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell">scrappie events reads <span class="o" style="font-weight: 600;">></span> test2.fa</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n</span> 1 test2.fa</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> test2.fa <span class="o" style="font-weight: 600;">]</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"Test 3"</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell">scrappie raw reads | <span class="nb" style="color: #0086b3;">tee </span>test2.fa | <span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'^>'</span> | <span class="nb" style="color: #0086b3;">cut</span> <span class="nt" style="color: #000080;">-d</span> <span class="s1" style="color: #d14;">' '</span> <span class="nt" style="color: #000080;">-f</span> 2- | python3 misc/json_to_tsv.py <span class="o" style="font-weight: 600;">></span> test3.tsv</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: #000080;">-s</span> test3.tsv <span class="o" style="font-weight: 600;">]</span></span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat </span>test3.tsv</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a#ac56e5cfa5a475febd17cd706f219a2cedec85e5"><strong>debian/tests/simple_test.py</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnapilib.apred</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">adapter_prediction</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">dnapilib.apred</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">iterative_adapter_prediction</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"></span>
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4
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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;">test_functional</span><span class="p">():</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">iterative_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iterative_adapter_prediction</span><span class="p">(</span><span class="s" style="color: #d14;">"good.fq"</span><span class="p">,</span> <span class="p">[</span><span class="mf" style="color: #099;">1.2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.3</span><span class="p">,</span> <span class="mf" style="color: #099;">1.4</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">],</span> <span class="mi" style="color: #099;">50000</span><span class="p">)</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"> <span class="n" style="color: #333;">single_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_prediction</span><span class="p">(</span><span class="s" style="color: #d14;">"good.fq"</span><span class="p">,</span> <span class="mf" style="color: #099;">1.4</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">50000</span><span class="p">)</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">iterative_result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TGGAATTCTCGG'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">single_result</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'TGGAATTCTCGGGTGCCAAGGAACTCC'</span><span class="p">)</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">iterative_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">iterative_adapter_prediction</span><span class="p">(</span><span class="s" style="color: #d14;">"processed.fq"</span><span class="p">,</span> <span class="p">[</span><span class="mf" style="color: #099;">1.2</span><span class="p">,</span> <span class="mf" style="color: #099;">1.3</span><span class="p">,</span> <span class="mf" style="color: #099;">1.4</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">11</span><span class="p">],</span> <span class="mi" style="color: #099;">50000</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">single_result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_prediction</span><span class="p">(</span><span class="s" style="color: #d14;">"processed.fq"</span><span class="p">,</span> <span class="mf" style="color: #099;">1.4</span><span class="p">,</span> <span class="mi" style="color: #099;">9</span><span class="p">,</span> <span class="mi" style="color: #099;">50000</span><span class="p">)</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">([</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">iterative_result</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'TCTGCCCAGTGCTCTG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TAATACTGCCTG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGGCAGTGTCTT'</span><span class="p">])</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">([</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">single_result</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'TAATACTGCCTGGTAATGATG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'TGGCAGTGTCTTAGCTGGTTG'</span><span class="p">,</span> <span class="s" style="color: #d14;">'CTGCCCAGTGCTCTGAA'</span><span class="p">])</span></span></pre>
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