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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/mindthegap">Debian Med / mindthegap</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/993c37580c255525182c540170e36ef613566f2b">993c3758</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-07T19:23:11Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage into package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mindthegap/commit/1c0e7138f82b96799827535d081dcaa3d9bce2c4">1c0e7138</a></strong>
<div>
<span>by Shayan Doust</span>
<i>at 2019-07-07T20:04:28Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Alter debian/copyright file and remove debian/doc-base till a more concrete documentation exists
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#9d9aaaac3f06acf1a05e3b67781afe64b64a22f7">
<span class="deleted-file">
−
debian/doc-base
</span>
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
</span>
</a>
</li>
<li class="file-stats">
<a href="#94883818a7e46d551608bfdf12f3c11a3ab81855">
<span class="new-file">
+
debian/mans/mindthegap.1
</span>
</a>
</li>
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<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/mindthegap/compare/3264dd3e79a2e044dcb22358ba01b1e66f3c6024...1c0e7138f82b96799827535d081dcaa3d9bce2c4#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: mindthegap</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Source: <path_to_download></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Comment: **** Before manually editing this file you should give ****</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> scan-copyrights</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> **** available in cme + lib-config-model-dpkg-perl ****</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> **** package a try. For existing copyright files try ****</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> cme update dpkg-copyright</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://github.com/GATB/MindTheGap</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Comment:</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Files: *</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">xx-20yy <upstream</span>></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">License: <span class="idiff left right"><license></span></span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Copyright: 20<span class="idiff left right">14 GATB <gatb.inria.fr</span>></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: <span class="idiff left right">GNU Affero General Public License v3.0</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Copyright: 2019 Shayan Doust <hello@shayandoust.me></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: <span class="idiff left right"><license></span></span></pre>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">License: <span class="idiff left right">GNU Affero General Public License v3.0</span></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Document: mindthegap</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Title: <title for this doc></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Author: <author of this doc></span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">Abstract: <if you have no better clue the short and</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> long description from debian/control might fit here as well></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">Section: Science/{Biology,Medicine} # see /usr/share/doc/doc-base/doc-base.txt.gz "2.3.3. The `section' field"</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"># pick one of the below options</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">Format: Text</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Files: /usr/share/doc/mindthegap/<pkg>.txt.gz</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">Format: html</span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Index: /usr/share/doc/mindthegap/html/index.html</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">Files: /usr/share/doc/mindthegap/html/*</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Format: pdf</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">Files: /usr/share/doc/mindthegap/<pkg>.pdf.gz</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Format: postscript</span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">Files: /usr/share/doc/mindthegap/<pkg>.ps.gz</span></pre>
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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/mindthegap/compare/3264dd3e79a2e044dcb22358ba01b1e66f3c6024...1c0e7138f82b96799827535d081dcaa3d9bce2c4#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/mans/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/mindthegap/compare/3264dd3e79a2e044dcb22358ba01b1e66f3c6024...1c0e7138f82b96799827535d081dcaa3d9bce2c4#94883818a7e46d551608bfdf12f3c11a3ab81855"><strong>debian/mans/mindthegap.1</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">.TH MINDTHEGAP 1</span>
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<td class="diff-line-num new new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">MindTheGap - Perform detection and assembly of DNA insertion variants</span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.B MindTheGap</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"><module> [module options]</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">MindTheGap is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. It takes as input a set of reads and a reference genome. It outputs two sets of FASTA sequences: one is the set of breakpoints of detected insertion sites, the other is the set of assembled insertions for each breakpoint.</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">MindTheGap can also be used as a genome assembly finishing tool: it can fill the gaps between a set of input contigs without any a priori on their relative order and orientation. It outputs the results in gfa file.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">\X'ps:'\c</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">find - insertion breakpoint detection. </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Usage:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.B MindTheGap</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">find ( -in </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.I <reads.fq></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">| -graph</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.I <graph.h5></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">) -ref</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.I <reference.fa></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">[option]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\X'ps:'\c</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">fill - gap-filler or insertion assembly</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">.br</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Usage:</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.B MindTheGap</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">fill ( -in </span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.I <reads.fq></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">| -graph</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">.I <graph.h5></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">) ( -bkpt </span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.I <breakpoints.fa></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">| -contig</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">.I <contig.fa></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">) [options]</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">.SH COMMON OPTIONS</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">help - display the MindTheGap help menu</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.br</span>
</pre>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">Usage:</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.B MindTheGap</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">-help</span>
</pre>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">.br</span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">\X'ps:'\c</span>
</pre>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.br</span>
</pre>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">version - display current version</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.br</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Usage:</span>
</pre>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.B MindTheGap</span>
</pre>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">-version</span></pre>
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