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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/pilon">Debian Med / pilon</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pilon/commit/1e0a80e1cfc9e301b74d751194bfa9d72d38b3cf">1e0a80e1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T06:36:07Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
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<strong><a href="https://salsa.debian.org/med-team/pilon/commit/c74f52df407444d33b82bc28a56f391820b09577">c74f52df</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-08-03T08:37:56Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Missuse ITP for pilon-non-free
</pre>
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<h4>4 changed files:</h4>
<ul>
<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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<li class="file-stats">
<a href="#1cb7bbaf0bb6ea80762a8dacf7cb8d437cf65eac">
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debian/pilon.1
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">pilon (1.22+dfsg-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">pilon (1.22+dfsg-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">903911</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> <span class="idiff left right">Thu, 23 Feb 2017 16:48:18 +01</span>00</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 03 Aug 2018 10:37:51 +02</span>00</span></pre>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577#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: teal;">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: navy;">-p</span> <span class="nv" style="color: teal;">$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: teal;">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 $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: teal;">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="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: teal;">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="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: teal;">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;">This manpage was written by </span><span class="nv" style="color: teal;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" 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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14
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<pre style="margin: 0;">+<span id="LC14" 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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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>pilon</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--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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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$NAME</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: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="se" style="color: #d14;">\</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/specifed/specified/'</span> <span class="se" style="color: #d14;">\</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"> <span class="nt" style="color: navy;">-e</span> <span class="s1" style="color: #d14;">'s/minumum/minimum/'</span> <span class="se" style="color: #d14;">\</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"> <span class="nv" style="color: teal;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</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;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: teal;">EOT</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;">Please enhance the help2man output.</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" 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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29
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<pre style="margin: 0;">+<span id="LC29" 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="LC30" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"></span></pre>
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<a href="https://salsa.debian.org/med-team/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577#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/pilon/compare/87abaab921e38d2ef911224c7f825e0b1cc70681...c74f52df407444d33b82bc28a56f391820b09577#1cb7bbaf0bb6ea80762a8dacf7cb8d437cf65eac"><strong>debian/pilon.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 1.47.6.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH PILON "1" "June 2018" "pilon 1.22" "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">pilon \- automated genome assembly improvement and variant detection tool</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 pilon</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fB\-\-genome\fR genome.fasta [\-\-frags frags.bam] [\-\-jumps jumps.bam] [\-\-unpaired unpaired.bam]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">[...other options...]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Pilon is a software tool which can be used to:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.IP \[bu] 2</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Automatically improve draft assemblies</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.IP \[bu]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Find variation among strains, including large event detection</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.P</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Pilon requires as input a FASTA file of the genome along with one or more</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">BAM files of reads aligned to the input FASTA file. Pilon uses read</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">alignment analysis to identify inconsistencies between the input genome and</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">the evidence in the reads. It then attempts to make improvements to the</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">input genome, including:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.IP \[bu] 2</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Single base differences</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.IP \[bu]</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Small indels</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.IP \[bu]</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Larger indel or block substitution events</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.IP \[bu]</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Gap filling</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.IP \[bu]</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Identification of local misassemblies, including optional opening of new gaps</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.SH OPTIONS</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.TP</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">\fB\-\-help\fR</span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.IP</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">for option details</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.SS INPUTS</span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.IP</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">\fB\-\-genome\fR genome.fasta</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">The input genome we are trying to improve, which must be the reference used</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">for the bam alignments. At least one of \fB\-\-frags\fR or \fB\-\-jumps\fR must also be given.</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">\fB\-\-frags\fR frags.bam</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">A bam file consisting of fragment paired\-end alignments, aligned to the \fB\-\-genome\fR</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">argument using bwa or bowtie2. This argument may be specified more than once.</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\fB\-\-jumps\fR jumps.bam</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">A bam file consisting of jump (mate pair) paired\-end alignments, aligned to the</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">\fB\-\-genome\fR argument using bwa or bowtie2. This argument may be specified more than once.</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">.IP</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">\fB\-\-unpaired\fR unpaired.bam</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.IP</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">A bam file consisting of unpaired alignments, aligned to the \fB\-\-genome\fR argument</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">using bwa or bowtie2. This argument may be specified more than once.</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.IP</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">\fB\-\-bam\fR any.bam</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">.IP</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">A bam file of unknown type; Pilon will scan it and attempt to classify it as one</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">of the above bam types.</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">.SS OUTPUTS</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.IP</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-\-output\fR prefix</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">.IP</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Prefix for output files</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">.IP</span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">\fB\-\-outdir\fR directory</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.IP</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Use this directory for all output files.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.IP</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">\fB\-\-changes\fR</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">.IP</span>
</pre>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">If specified, a file listing changes in the <output>.fasta will be generated.</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.IP</span>
</pre>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">\fB\-\-vcf\fR</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">.IP</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">If specified, a vcf file will be generated</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.IP</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">\fB\-\-vcfqe\fR</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">.IP</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">If specified, the VCF will contain a QE (quality\-weighted evidence) field rather</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">than the default QP (quality\-weighted percentage of evidence) field.</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">.IP</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">\fB\-\-tracks\fR</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">.IP</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">This options will cause many track files (*.bed, *.wig) suitable for viewing in</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">a genome browser to be written.</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">.SS CONTROL</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">.IP</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">\fB\-\-variant\fR</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">.IP</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">Sets up heuristics for variant calling, as opposed to assembly improvement;</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">equivalent to "\-\-vcf \fB\-\-fix\fR all,breaks".</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">.IP</span>
</pre>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">\fB\-\-chunksize\fR</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">.IP</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">Input FASTA elements larger than this will be processed in smaller pieces not to</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">exceed this size (default 10000000).</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">.IP</span>
</pre>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">\fB\-\-diploid\fR</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">.IP</span>
</pre>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">Sample is from diploid organism; will eventually affect calling of heterozygous SNPs</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">.IP</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">\fB\-\-fix\fR fixlist</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">.IP</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">A comma\-separated list of categories of issues to try to fix:</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">.IP</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">"snps": try to fix individual base errors;</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">"indels": try to fix small indels;</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">"gaps": try to fill gaps;</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">"local": try to detect and fix local misassemblies;</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">"all": all of the above (default);</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">"bases": shorthand for "snps" and "indels" (for back compatibility);</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">"none": none of the above; new fasta file will not be written.</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">.IP</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">The following are experimental fix types:</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">.IP</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">"amb": fix ambiguous bases in fasta output (to most likely alternative);</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">"breaks": allow local reassembly to open new gaps (with "local");</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">"circles": try to close circlar elements when used with long corrected reads;</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">"novel": assemble novel sequence from unaligned non\-jump reads.</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">.IP</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">\fB\-\-dumpreads\fR</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">.IP</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">Dump reads for local re\-assemblies.</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">.IP</span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">\fB\-\-duplicates\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">.IP</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">Use reads marked as duplicates in the input BAMs (ignored by default).</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">\fB\-\-iupac\fR</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">.IP</span>
</pre>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">Output IUPAC ambiguous base codes in the output FASTA file when appropriate.</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">\fB\-\-nonpf\fR</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">.IP</span>
</pre>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">Use reads which failed sequencer quality filtering (ignored by default).</span>
</pre>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">.IP</span>
</pre>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">\fB\-\-targets\fR targetlist</span>
</pre>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">.IP</span>
</pre>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">Only process the specified target(s).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">Targets are comma\-separated, and each target</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">is a fasta element name optionally followed by a base range.</span>
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<td class="diff-line-num new new_line" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">Example: "scaffold00001,scaffold00002:10000\-20000" would result in processing all of</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">scaffold00001 and coordinates 10000\-20000 of scaffold00002.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">If "targetlist" is the name of a file, each line will be treated as a target</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">specification.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new old_line" 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="diff-line-num new new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">\fB\-\-threads\fR</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">Degree of parallelism to use for certain processing (default 1). Experimental.</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">\fB\-\-verbose\fR</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">.IP</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">More verbose output.</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">\fB\-\-debug\fR</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num new new_line" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">Debugging output (implies verbose).</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">.IP</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">\fB\-\-version\fR</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">.IP</span>
</pre>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">Print version string and exit.</span>
</pre>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">.SS HEURISTICS:</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">\fB\-\-defaultqual\fR qual</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">Assumes bases are of this quality if quals are no present in input BAMs (default 15).</span>
</pre>
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<td class="diff-line-num new new_line" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">\fB\-\-flank\fR nbases</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">Controls how much of the well\-aligned reads will be used; this many bases at each</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">end of the good reads will be ignored (default 10).</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">\fB\-\-gapmargin\fR</span>
</pre>
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<td class="diff-line-num new new_line" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">Closed gaps must be within this number of bases of true size to be closed (100000)</span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">.IP</span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">\fB\-\-K\fR</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">.IP</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">Kmer size used by internal assembler (default 47).</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">.IP</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">\fB\-\-mindepth\fR depth</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">Variants (snps and indels) will only be called if there is coverage of good pairs</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">at this depth or more; if this value is >= 1, it is an absolute depth, if it is a</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">fraction < 1, then minimum depth is computed by multiplying this value by the mean</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">coverage for the region, with a minimum value of 5 (default 0.1: min depth to call</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">is 10% of mean coverage or 5, whichever is greater).</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">.IP</span>
</pre>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">\fB\-\-mingap\fR</span>
</pre>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">Minimum size for unclosed gaps (default 10)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">\fB\-\-minmq\fR</span>
</pre>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">Minimum alignment mapping quality for a read to count in pileups (default 0)</span>
</pre>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">\fB\-\-minqual\fR</span>
</pre>
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<td class="diff-line-num new old_line" 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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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">.IP</span>
</pre>
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<td class="diff-line-num new new_line" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">Minimum base quality to consider for pileups (default 0)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">.IP</span>
</pre>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">\fB\-\-nostrays\fR</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">Skip making a pass through the input BAM files to identify stray pairs, that is,</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">those pairs in which both reads are aligned but not marked valid because they have</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">inconsistent orientation or separation. Identifying stray pairs can help fill gaps</span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">and assemble larger insertions, especially of repeat content. However, doing so</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">sometimes consumes considerable memory.</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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