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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/surpyvor">Debian Med / surpyvor</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/surpyvor/-/commit/62f3a35ce977175483413c1731ceb13c9359254e">62f3a35c</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-13T19:43:22+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add python3-upsetplot to Depends
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<strong><a href="https://salsa.debian.org/med-team/surpyvor/-/commit/55e6f42de606bc592bafb769cd2cd7b03a80f4b1">55e6f42d</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2021-07-13T14:20:12+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add manpage
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<strong><a href="https://salsa.debian.org/med-team/surpyvor/-/commit/84af058bb84982975990bb172e64760d298c83b0">84af058b</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-13T19:56:27+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">d/control: Minor fix
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<strong><a href="https://salsa.debian.org/med-team/surpyvor/-/commit/530f6ff641ddec7bad78fec429127783e289a0af">530f6ff6</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2021-07-13T19:57:10+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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+
debian/createmanpages
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<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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debian/manpages
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<a href="#a3920d3fb67251bf78430e15b47f7a38f02801c3">
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debian/surpyvor.1
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">surpyvor (0.5-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">surpyvor (0.5-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #990883)</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> <span class="idiff left">Sat</span>, 1<span class="idiff">0</span> Jul 2021 <span class="idiff">00:01:07</span> +0<span class="idiff right">20</span>0</span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> <span class="idiff left">Tue</span>, 1<span class="idiff">3</span> Jul 2021 <span class="idiff">19:52:30</span> +0<span class="idiff right">53</span>0</span></pre>
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<a href="https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -21,13 +21,14 @@ Depends:</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> python3-cyvcf2,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> python3-matplotlib-venn,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> survivor,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-upsetplot,</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Description: modification of VCF files with SURVIVOR</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> SURVIVOR is a tool set for simulating/evaluating</span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> structural varia<span class="idiff left right">n</span>tions, merging and comparing SVs within</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> structural variations, merging and comparing SVs within</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> and among samples, and includes various methods to</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext"> reformat or summarize structural varia<span class="idiff left right">n</span>tions.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> reformat or summarize structural variations.</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> This package provides a Python wrapper to help with its</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> integration in various Python-based workflows.</span></pre>
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<a href="https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af#ebcf9854ee19af4b7bf8405b283789c18769680f"><strong>debian/createmanpages</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/sh</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nv" style="color: #008080;">MANDIR</span><span class="o" style="font-weight: 600;">=</span>debian</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: #000080;">-p</span> <span class="nv" style="color: #008080;">$MANDIR</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="nv" style="color: #008080;">VERSION</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span>dpkg-parsechangelog | <span class="nb" style="color: #0086b3;">awk</span> <span class="s1" style="color: #d14;">'/^Version:/ {print $2}'</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/^[0-9]*://'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/-.*//'</span> <span class="nt" style="color: #000080;">-e</span> <span class="s1" style="color: #d14;">'s/[+~]dfsg$//'</span><span class="sb" style="color: #d14;">`</span></span>
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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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10
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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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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span>surpyvor</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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"> <span class="nt" style="color: #000080;">--version-string</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$VERSION</span><span class="s2" style="color: #d14;">"</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span> <span class="o" style="font-weight: 600;">></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$AUTHOR</span> <span class="o" style="font-weight: 600;">>></span> <span class="nv" style="color: #008080;">$MANDIR</span>/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"></span>
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24
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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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25
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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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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="sh" style="color: #d14;">The following web page might be helpful in doing so:</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"><span class="sh" style="color: #d14;"> http://liw.fi/manpages/</span></span>
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28
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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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<a href="https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af#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/*.1</span></pre>
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<a href="https://salsa.debian.org/med-team/surpyvor/-/compare/38ffe8416adc05ed856d761b844a04f258559cda...530f6ff641ddec7bad78fec429127783e289a0af#a3920d3fb67251bf78430e15b47f7a38f02801c3"><strong>debian/surpyvor.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 1.47.16.</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH SURPYVOR "1" "July 2021" "surpyvor 0.5" "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">surpyvor \- modification of VCF files with SURVIVOR</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">.SH DESCRIPTION</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">usage: surpyvor [\-h] [\-v] {merge,highsens,highconf,prf,venn,upset} ...</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">.PP</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">A wrapper around SURVIVOR, with convenience functions.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.SS "optional arguments:"</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.TP</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">\fB\-h\fR, \fB\-\-help\fR</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">show this help message and exit</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">.TP</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">\fB\-v\fR, \fB\-\-version\fR</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Print version and quit.</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">.SS "[sub-commands]:"</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">.IP</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">{merge,highsens,highconf,prf,venn,upset}</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">.TP</span>
</pre>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">merge</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">merging vcf files of SVs</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">highsens</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">get union of SV vcfs</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">highconf</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">get intersection of SV vcfs</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">prf</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">calculate precision, recall and F\-measure</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">.TP</span>
</pre>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">venn</span>
</pre>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Make venn diagram for 2 or 3 SV vcf files</span>
</pre>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">.TP</span>
</pre>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">upset</span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Make upset plot for multiple SV vcf files</span>
</pre>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC38" 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="LC39" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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