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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/lighter">Debian Med / lighter</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/44de835eaa6f2f22040944494700f57c59e80b71">44de835e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T22:36:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ITP bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/b8ae51a782b9e22b6dc3493635a5205f3005c30b">b8ae51a7</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T22:39:03+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/lighter/-/commit/ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41">ebdc5fb9</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T22:41:59+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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<li class="file-stats">
<a href="#6291b8126047e99f6f703f1c75aa9277f11d94f5">
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+
debian/lighter.1
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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+
debian/manpages
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/lighter/-/compare/8cdccd4b023e2f0c023895b58e4298a609d116ba...ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">lighter (1.1.2-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">lighter (1.1.2-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right"><bug></span>)</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<span class="idiff left right">961665</span>)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 27 May 2020 <span class="idiff left right">15:51:3</span>0 +0200</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 27 May 2020 <span class="idiff left right">22:39:1</span>0 +0200</span></pre>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/lighter/-/compare/8cdccd4b023e2f0c023895b58e4298a609d116ba...ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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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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<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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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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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<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;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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18
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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;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$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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21
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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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27
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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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<li id="6291b8126047e99f6f703f1c75aa9277f11d94f5">
<a href="https://salsa.debian.org/med-team/lighter/-/compare/8cdccd4b023e2f0c023895b58e4298a609d116ba...ebdc5fb9938ad01ef9b6a41703315dd1bdce1f41#6291b8126047e99f6f703f1c75aa9277f11d94f5"><strong>debian/lighter.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 1.47.15.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH LIGHTER "1" "May 2020" "lighter 1.1.2" "User Commands"</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">.SH NAME</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">lighter \- fast and memory-efficient sequencing error corrector</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B lighter</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,OPTIONS\/\fR]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Lighter is a fast, memory-efficient tool for correcting sequencing</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">filters, one holding a sample of the input k-mers and the other holding</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">k-mers likely to be correct. As long as the sampling fraction is</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">adjusted in inverse proportion to the depth of sequencing, Bloom filter</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">size can be held constant while maintaining near-constant accuracy.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Lighter is parallelized, uses no secondary storage, and is both faster</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">and more memory-efficient than competing approaches while achieving</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">comparable accuracy.</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.SH OPTIONS:</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.SS Required parameters:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-r\fR seq_file: seq_file is the path to the sequence file. Can use multiple \fB\-r\fR to specifiy multiple sequence files</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">The file can be fasta and fastq, and can be gzip'ed with extension *.gz.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">When the input file is *.gz, the corresponding output file will also be gzip'ed.</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-k\fR kmer_length genome_size alpha: (see README for information on setting alpha)</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">or</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">\fB\-K\fR kmer_length genom_size: in this case, the genome size should be relative accurate.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.SS "Other parameters:"</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">\fB\-od\fR output_file_directory: (default: ./)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-t\fR num_of_threads: number of threads to use (default: 1)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">\fB\-maxcor\fR INT: the maximum number of corrections within a 20bp window (default: 4)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-trim\fR: allow trimming (default: false)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-discard\fR: discard unfixable reads. Will LOSE paired\-end matching when discarding (default: false)</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-noQual\fR: ignore the quality socre (default: false)</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-newQual\fR ascii_quality_score: set the quality for the bases corrected to the specified score (default: not used)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">\fB\-saveTrustedKmers\fR file: save the trusted kmers to specified file then stop (default: not used)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-loadTrustedKmers\fR file: directly get solid kmers from specified file (default: not used)</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">\fB\-zlib\fR compress_level: set the compression level(0\-9) of gzip (default: 1)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-h\fR: print the help message and quit</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-v\fR: print the version information and quit</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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