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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/vcfanno">Debian Med / vcfanno</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcfanno/-/commit/4aa98312720a95744ef57655d803ab5e11d2d76c">4aa98312</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-18T02:57:38+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcfanno/-/commit/66d4559a8b8a396d04f9bfb6be6a3bc6ea4c77d1">66d4559a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-18T02:58:03+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Change arch of examples package to all
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
<span class="new-file">
+
debian/createmanpages
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</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
<span class="new-file">
+
debian/manpages
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</a>
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<li class="file-stats">
<a href="#2a4e7f66f8a6b3b8c9091b7544f3103d92fa3d7c">
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+
debian/vcfanno.1
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/199741cc61fada0e121c6cb8b921f3b3529a27f0...66d4559a8b8a396d04f9bfb6be6a3bc6ea4c77d1#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" 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">@@ -46,10 +46,9 @@ Description: annotate a VCF with other VCFs/BEDs/tabixed files</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> second using 12 processes on a server.</span>
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<td class="diff-line-num old_line" data-linenumber="47" 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="47" 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="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Package: vcfanno-examples</span>
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<td class="diff-line-num old old_line" data-linenumber="49" 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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<td class="diff-line-num new_line old" data-linenumber="49" 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="LC49" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ny</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Architecture: a<span class="idiff left right">ll</span></span>
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<td class="diff-line-num new_line" data-linenumber="50" 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="LC50" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">Built-Using: ${misc:Built-Using}</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">Description: examples for vcfanno: annotate a VCF with other VCFs/BEDs/tabixed files</span>
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<td class="diff-line-num old_line" data-linenumber="54" 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="LC53" class="line" lang="plaintext"> Vcfanno allows you to quickly annotate your VCF with any number of INFO</span>
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<td class="diff-line-num old_line" data-linenumber="55" 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="54" 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="LC54" class="line" lang="plaintext"> fields from any number of VCFs or BED files. It uses a simple conf file</span>
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<li id="ebcf9854ee19af4b7bf8405b283789c18769680f">
<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/199741cc61fada0e121c6cb8b921f3b3529a27f0...66d4559a8b8a396d04f9bfb6be6a3bc6ea4c77d1#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<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">
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nv" style="color: #008080;">NAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Description:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Description: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="nv" style="color: #008080;">PROGNAME</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="s2" style="color: #d14;">"^Package:"</span> debian/control | <span class="nb" style="color: #0086b3;">sed</span> <span class="s1" style="color: #d14;">'s/^Package: *//'</span> | <span class="nb" style="color: #0086b3;">head</span> <span class="nt" style="color: #000080;">-n1</span><span class="sb" style="color: #d14;">`</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"><span class="nv" style="color: #008080;">AUTHOR</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">".SH AUTHOR</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="s2" style="color: #d14;">This manpage was written by </span><span class="nv" style="color: #008080;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>vcfanno</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">help2man <span class="nt" style="color: #000080;">--no-info</span> <span class="nt" style="color: #000080;">--no-discard-stderr</span> <span class="nt" style="color: #000080;">--help-option</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-h"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #000080;">--name</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$NAME</span><span class="s2" style="color: #d14;">"</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$MANDIR</span><span class="s2" style="color: #d14;">/*.1"</span> <span class="o" style="font-weight: 600;">></span> debian/manpages</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cat</span> <span class="o" style="font-weight: 600;"><<</span><span class="no" style="color: #008080;">EOT</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="sh" style="color: #d14;">Please enhance the help2man output.</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell"><span class="no" style="color: #008080;">EOT</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="shell"></span></pre>
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<li id="68e0b13744e158347bfd74ebaaca667435f07d14">
<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/199741cc61fada0e121c6cb8b921f3b3529a27f0...66d4559a8b8a396d04f9bfb6be6a3bc6ea4c77d1#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/vcfanno/-/compare/199741cc61fada0e121c6cb8b921f3b3529a27f0...66d4559a8b8a396d04f9bfb6be6a3bc6ea4c77d1#2a4e7f66f8a6b3b8c9091b7544f3103d92fa3d7c"><strong>debian/vcfanno.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 1.47.12.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH VCFANNO "1" "July 2020" "vcfanno 0.3.2+ds" "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">vcfanno \- annotate a VCF with other VCFs/BEDs/tabixed files</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">=============================================</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">vcfanno version 0.3.2 [built with go1.14.4]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.PP</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">see: https://github.com/brentp/vcfanno</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">=============================================</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Usage of vcfanno:</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">\fB\-base\-path\fR string</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">optional base\-path to prepend to annotation files in the config</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">\fB\-ends\fR</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">annotate the start and end as well as the interval itself.</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">\fB\-lua\fR string</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">optional path to a file containing custom javascript functions to be used as ops</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">\fB\-p\fR int</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">number of processes to use. (default 2)</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">.HP</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">\fB\-permissive\-overlap\fR</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">.IP</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">annotate with an overlapping variant even it doesn't share the same ref and alt alleles. Default is to require exact match between variants.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> This manpage was written by Nilesh Patra for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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