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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/bio-rainbow">Debian Med / bio-rainbow</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/06adcdfa0af15a53821bfdcf143daf9fdbb5d5ab">06adcdfa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T15:41:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add rudimentary manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/b2cdf22d96ec5e61145bb155d81f91769bb89219">b2cdf22d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T15:53:31+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">spelling, do not override dh_installman
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/3e3bb431b3d3234dcd54913b8c370c1cdad61e2a">3e3bb431</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-07-04T16:12:32+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Sort out some issues with manpages
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/bio-rainbow/commit/6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de">6a9c7fa6</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-07-04T16:13:36+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
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<h4>14 changed files:</h4>
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<li class="file-stats">
<a href="#7f4d553edd5c0cf8dca44c702fc4c29142638d1f">
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debian/bio-rainbow.manpages
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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debian/createmanpages
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debian/manpages
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debian/mans/bio-rainbow.1
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debian/mans/ezmsim.1
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debian/mans/rbasm.1
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debian/mans/select_all_rbcontig.pl.1
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debian/mans/select_best_rbcontig.pl.1
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debian/mans/select_best_rbcontig_plus_read1.pl.1
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debian/mans/select_sec_rbcontig.pl.1
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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debian/patches/spelling.patch
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="7f4d553edd5c0cf8dca44c702fc4c29142638d1f">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#7f4d553edd5c0cf8dca44c702fc4c29142638d1f"><strong>debian/bio-rainbow.manpages</strong>
deleted
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bio-rainbow.1</span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">bio-rainbow (2.0.4+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bio-rainbow (2.0.4+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,8 +17,10 @@ bio-rainbow (2.0.4+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * DEP3</span>
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<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * DEP5</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * hardening=+all</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> * Add rudimentary manpages</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * spelling</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 04 Jul 2018 1<span class="idiff left right">4:39:26</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 04 Jul 2018 1<span class="idiff left right">6:12:39</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">bio-rainbow (2.0.4-1) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#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/mans</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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<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;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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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;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>ezmsim</span>
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22
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<pre style="margin: 0;">+<span id="LC22" 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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" 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;">"simulate enzyme cut assembly sequences"</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="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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25
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<pre style="margin: 0;">+<span id="LC25" 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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>rbasm</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" -h"</span> <span class="se" style="color: #d14;">\</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"local assemble fragments around restriction sites"</span> <span class="se" style="color: #d14;">\</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$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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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="shell"></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>select_all_rbcontig.pl</span>
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34
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<pre style="margin: 0;">+<span id="LC34" 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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"select all rbcontig"</span> <span class="se" style="color: #d14;">\</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" 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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37
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<pre style="margin: 0;">+<span id="LC37" 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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="shell"></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>select_best_rbcontig.pl</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="shell">help2man <span class="nt" style="color: navy;">--no-info</span> <span class="nt" style="color: navy;">--no-discard-stderr</span> <span class="nt" style="color: navy;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"select best rbcontig"</span> <span class="se" style="color: #d14;">\</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="shell"> <span class="nt" style="color: navy;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="shell"></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>select_best_rbcontig_plus_read1.pl</span>
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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"select best rbcontig plus read1"</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="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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49
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<pre style="margin: 0;">+<span id="LC49" 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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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="shell"></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"><span class="nv" style="color: teal;">progname</span><span class="o" style="font-weight: 600;">=</span>select_sec_rbcontig.pl</span>
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52
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<pre style="margin: 0;">+<span id="LC52" 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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell"> <span class="nt" style="color: navy;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"select second rbcontig"</span> <span class="se" style="color: #d14;">\</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" 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;">${</span><span class="nv" style="color: teal;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: teal;">$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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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$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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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"></span>
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59
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<pre style="margin: 0;">+<span id="LC59" 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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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"><span class="no" style="color: teal;">EOT</span></span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#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/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#80caaeee58d44580fe4180ae1e4fc5eb4ffc39ff"><strong>debian/mans/bio-rainbow.1</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH BIO-RAINBOW "1" "July 2018" "bio-rainbow 2.0.4" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bio-rainbow \- clustering and assembling short reads for bioinformatics</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B rainbow</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<cmd> \/\fR[\fI\,options\/\fR]</span>
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8
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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">rainbow 2.0.4 \fB\-\-\fR <ruanjue@gmail.com, chongzechen@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">cluster</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Input File Format: paired fasta/fastq file(s)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">\fB\-1\fR <string> Input fasta/fastq file, supports multiple '\-1'</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-2\fR <string> Input fasta/fastq file, supports multiple '\-2' [null]</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">\fB\-l\fR <int></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Read length, default: 0 variable</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.TP</span>
</pre>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">\fB\-m\fR <int></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Maximum mismatches [4]</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">.TP</span>
</pre>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">\fB\-e\fR <int></span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Exactly matching threshold [2000]</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.TP</span>
</pre>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-L\fR</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Low level of polymorphism</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.IP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">div</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">.PP</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string></span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">Output File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">.HP</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">\fB\-i\fR <string> Input file [stdin]</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">.HP</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">\fB\-o\fR <string> Output file [stdout]</span>
</pre>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">.TP</span>
</pre>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">\fB\-k\fR <int></span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">K_allele, min variants to create a new group [2]</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">.TP</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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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">\fB\-K\fR <int></span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">K_allele, divide regardless of frequency when num of variants exceed this value [50]</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">.TP</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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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">\fB\-f\fR <float></span>
</pre>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Frequency, min variant frequency to create a new group [0.2]</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">.IP</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">merge</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.PP</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Input File Format: <seqid:int>\et<cluster_id:int>\et<read1:string>\et<read2:string>[\et<pre_cluster_id:int>]</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">.HP</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">\fB\-i\fR <string> Input rbasm output file [stdin]</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">.TP</span>
</pre>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">\fB\-a\fR</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">output assembly</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">.HP</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">\fB\-o\fR <string> Output file for merged contigs, one line per cluster [stdout]</span>
</pre>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">\fB\-N\fR <int></span>
</pre>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">Maximum number of divided clusters to merge [300]</span>
</pre>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">\fB\-l\fR <int></span>
</pre>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Minimum overlap when assemble two reads (valid only when '\-a' is opened) [5]</span>
</pre>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
</pre>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">\fB\-f\fR <float></span>
</pre>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">Minimum fraction of similarity when assembly (valid only when '\-a' is opened) [0.90]</span>
</pre>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.TP</span>
</pre>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">\fB\-r\fR <int></span>
</pre>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">Minimum number of reads to assemble (valid only when '\-a' is opened) [5]</span>
</pre>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">\fB\-R\fR <int></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">Maximum number of reads to assemble (valid only when '\-a' is opened) [300]</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC76" 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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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#f449de9c9efd6d280e2f1a476a01ba2e4e349219"><strong>debian/mans/ezmsim.1</strong></a>
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1
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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 EZMSIM "1" "July 2018" "ezmsim 2.0.4" "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">ezmsim \- simulate enzyme cut assembly sequences</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 ezmsim</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<LR|EF> \/\fR[\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">Program: ezmsim (simulate enzyme cut assembly sequences)</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Version: 0.1.1</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Contact: Zechen Chong <chongzechen@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Options: LR simulate LR reads</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">RAD</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">simulate RAD reads</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC18" 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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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#de6871b452bf4336faf51c949c03676f779e84ba"><strong>debian/mans/rbasm.1</strong></a>
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1
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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 RBASM "1" "July 2018" "rbasm 2.0.4" "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">rbasm \- local assemble fragments around restriction sites</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B ef</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">[\fI\,options\/\fR]</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Local assemble fragments around restriction sites</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.HP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-i\fR <string> Input file [STDIN]</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.HP</span>
</pre>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-o\fR <string> Output file [STDOUT]</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.TP</span>
</pre>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">\fB\-l\fR <int></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Minimum length of overlap [5]</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.TP</span>
</pre>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">\fB\-s\fR <float></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Minimum similiarity of overlap [0.90]</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.TP</span>
</pre>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-r\fR <int></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Minimum reads to execute assembly [5]</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">.TP</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">\fB\-R\fR <int></span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Maximum reads to execute assembly [200]</span>
</pre>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.SH AUTHOR</span>
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27
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<pre style="margin: 0;">+<span id="LC27" 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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<li id="2152f18cfe0987d710421c3fe577dc074a044b43">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#2152f18cfe0987d710421c3fe577dc074a044b43"><strong>debian/mans/select_all_rbcontig.pl.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 SELECT_ALL_RBCONTIG.PL "1" "July 2018" "select_all_rbcontig.pl 2.0.4" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">select_all_rbcontig.pl \- select all rbcontig</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B select_all_rbcontig.pl</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<rbasmed file>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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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">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC11" 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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<li id="1bfb07b9766b80633ae1f9a481736b0ddb14ef02">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#1bfb07b9766b80633ae1f9a481736b0ddb14ef02"><strong>debian/mans/select_best_rbcontig.pl.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 SELECT_BEST_RBCONTIG.PL "1" "July 2018" "select_best_rbcontig.pl 2.0.4" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">select_best_rbcontig.pl \- select best rbcontig</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B select_best_rbcontig.pl</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<rbasmed file>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC11" 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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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#823ea5dc6aa8016d73e5634d0768407cab9b5b49"><strong>debian/mans/select_best_rbcontig_plus_read1.pl.1</strong></a>
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1
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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 SELECT_BEST_RBCONTIG_PLUS_READ1.PL "1" "July 2018" "select_best_rbcontig_plus_read1.pl 2.0.4" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">select_best_rbcontig_plus_read1.pl \- select best rbcontig plus read1</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B select_best_rbcontig_plus_read1.pl</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<rbasmed file> <rbdiv output file>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC11" 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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<li id="84f655a102765340b6d65696bd0bbd3fd2d736b3">
<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#84f655a102765340b6d65696bd0bbd3fd2d736b3"><strong>debian/mans/select_sec_rbcontig.pl.1</strong></a>
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1
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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 SELECT_SEC_RBCONTIG.PL "1" "July 2018" "select_sec_rbcontig.pl 2.0.4" "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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">select_sec_rbcontig.pl \- select second rbcontig</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH SYNOPSIS</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">.B select_sec_rbcontig.pl</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">\fI\,<rbasmed file>\/\fR</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH DESCRIPTION</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC11" 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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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">add_hardening.patch</span>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">rename_binary.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Wed, 04 Jul 2018 14:39:26 +0200</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: spelling</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.txt</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -93,10 +93,10 @@ NOTE: the input file format should be: <</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> Usage: rbasm [options]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> -i <string> Input file [STDIN] </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> -o <string> Output file [STDOUT]</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -l <int> Minium length of overlap [5]</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -s <float> Minium similiarity of overlap [0.90]</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -r <int> Minium reads to execute assembly [5]</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -R <int> Maxium reads to execute assembly [200]</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -l <int> Minimum length of overlap [5]</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -s <float> Minimum similiarity of overlap [0.90]</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -r <int> Minimum reads to execute assembly [5]</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -R <int> Maximum reads to execute assembly [200]</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> ----------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> <Obsoleted> rbmergetag: a program merges divided results to evaluate clustering performance.</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/asm_R2.c</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/asm_R2.c</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -397,10 +397,10 @@ int ef_usage(){</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> "Usage: ef [options]\n"</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> " -i <string> Input file [STDIN]\n"</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> " -o <string> Output file [STDOUT]\n"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" -l <int> Minium length of overlap [5]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" -s <float> Minium similiarity of overlap [0.90]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" -r <int> Minium reads to execute assembly [5]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-" -R <int> Maxium reads to execute assembly [200]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" -l <int> Minimum length of overlap [5]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" -s <float> Minimum similiarity of overlap [0.90]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" -r <int> Minimum reads to execute assembly [5]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+" -R <int> Maximum reads to execute assembly [200]\n"</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> "\n"</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> );</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> return 1;</span></pre>
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<a href="https://salsa.debian.org/med-team/bio-rainbow/compare/eda88020e0f07eea2738ba101f5751b16fb0eaf1...6a9c7fa6a02114ebb63b571c4e6bb6cdb37593de#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -9,18 +9,9 @@ include /usr/share/dpkg/default.mk</td>
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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">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</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"># see ENVIRONMENT in dpkg-buildflags(1)</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"># package maintainers to append CFLAGS</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"># package maintainers to append LDFLAGS</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">#export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num old old_line" data-linenumber="19" 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">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"># main packaging script based on dh7 syntax</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
20
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">%:</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
21
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh $@ </span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
23
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">override_dh_installman:</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> help2man --no-discard-stderr ./bio-rainbow > bio-rainbow.1</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> dh_installman</span>
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26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"></span></pre>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> # dh_installman is messing up .sh extension as language extension</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> dh_install debian/mans/*.1 usr/share/man/man1</span></pre>
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