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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/vt">Debian Med / vt</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/65dbddcf607858053817842eb7a27e6eb51569f9">65dbddcf</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-18T11:29:50+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add publication and Conda id
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/077a8a07923afeaf8a0d73871355d58aa73f9868">077a8a07</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-18T11:34:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Enhance long description from publication abstract giving more relevant for users than technical details what was used for linking
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/8dd227cac1d159aa98765ad1af7682d92788f78c">8dd227ca</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-18T11:52:23+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add more verbose test using example data
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vt/-/commit/f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b">f73a6884</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-18T11:59:28+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add simple manpage
</pre>
</li>
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<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<span class="new-file">
+
debian/README.test
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#ebcf9854ee19af4b7bf8405b283789c18769680f">
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debian/createmanpages
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<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
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debian/manpages
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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debian/tests/run-unit-test
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
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+
debian/upstream/metadata
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<li class="file-stats">
<a href="#05f831c95badbbd44a8b9fc0d564b54745f0810a">
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+
debian/vt-examples.install
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<li class="file-stats">
<a href="#9ef2917f6f883e279b64e7a65b915ab3d66f2e65">
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debian/vt.1
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<li class="file-stats">
<a href="#18136fb9a01e6e02e465c82dd6d0fbbf2dbc77b9">
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debian/vt.docs
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<li class="file-stats">
<a href="#b31cc3cfe4f5271b1de8b9b944d23573fccece23">
debian/install
→
debian/vt.install
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</ul>
<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"> <span class="nx">apt</span> <span class="nx">install</span> <span class="nx">vt</span><span class="o" style="font-weight: 600;">-</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" 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>
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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">@@ -27,10 +27,26 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> r-base-core,</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Description: <span class="idiff left right">Tool </span>set for short variant discovery in genetic sequence data</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Description: <span class="idiff left right">tool</span>set for short variant discovery in genetic sequence data</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> vt is a variant tool set that discovers short variants from Next Generation</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> Sequencing data.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext"> Visit http://genome.sph.umich.edu/wiki/vt for instructions.</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> Vt-normalize is a tool to normalize representation of genetic variants in</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> the VCF. Variant normalization is formally defined as the consistent</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> representation of genetic variants in an unambiguous and concise way. In</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> vt a simple general algorithm to enforce this is implemented.</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Package: vt-examples</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Enhances: vt</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Description: toolset for short variant discovery in genetic sequence data (examples)</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> vt is a variant tool set that discovers short variants from Next Generation</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> Sequencing data.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> Vt-normalize is a tool to normalize representation of genetic variants in</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> the VCF. Variant normalization is formally defined as the consistent</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> representation of genetic variants in an unambiguous and concise way. In</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> vt a simple general algorithm to enforce this is implemented.</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext"> <span class="idiff left right">vt uses htslib, tclap, Rmath, pcre2 and libsvm</span>.</span></pre>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> <span class="idiff left right">This package contains some example data</span>.</span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#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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<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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<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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<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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<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;">$DEBFULLNAME</span><span class="s2" style="color: #d14;"> for the Debian distribution and</span><span class="se" style="color: #d14;">\n</span><span class="s2" style="color: #d14;"> </span><span class="se" style="color: #d14;">\</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"><span class="s2" style="color: #d14;">can be used for any other usage of the program.</span><span class="se" style="color: #d14;">\</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="s2" style="color: #d14;">"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># If program name is different from package name or title should be</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># different from package short description change this here</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nv" style="color: #008080;">progname</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">PROGNAME</span><span class="k" style="font-weight: 600;">}</span></span>
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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;">" "</span> <span class="se" style="color: #d14;">\</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"> <span class="nt" style="color: #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;">${</span><span class="nv" style="color: #008080;">progname</span><span class="k" style="font-weight: 600;">}</span>.1</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="nv" style="color: #008080;">$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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<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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<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></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#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/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Tests: basic</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Depends: vt</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: basic, run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>vt</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell">find <span class="nb" style="color: #0086b3;">.</span> <span class="se" style="color: #d14;">\(</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.vcf.gz"</span> <span class="nt" style="color: #000080;">-o</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.gzi.gz"</span> <span class="nt" style="color: #000080;">-o</span> <span class="nt" style="color: #000080;">-name</span> <span class="s2" style="color: #d14;">"*.sh.gz"</span> <span class="se" style="color: #d14;">\)</span> <span class="nt" style="color: #000080;">-exec</span> <span class="nb" style="color: #0086b3;">gunzip</span> <span class="se" style="color: #d14;">\{\}</span> <span class="se" style="color: #d14;">\;</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-i</span> <span class="s1" style="color: #d14;">'s:VT=${DIR}/../vt:VT=/usr/bin/vt:'</span> test.sh</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell">bash ./test.sh</span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> Author: Adrian Tan and Gonçalo R. Abecasis and Hyun Min Kang</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Unified representation of genetic variants</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: Bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2015</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 31</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 13</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: 2202–2204</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1093/bioinformatics</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID: 25701572</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> PMCID: PMC4481842</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> URL: https://academic.oup.com/bioinformatics/article/31/13/2202/196142</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> eprint: https://academic.oup.com/bioinformatics/article-pdf/31/13/2202/17122489/btv112.pdf</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Registry:</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> - Name: conda:bioconda</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> Entry: vt</span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#05f831c95badbbd44a8b9fc0d564b54745f0810a"><strong>debian/vt-examples.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">test</span><span class="o" style="font-weight: 600;">/*</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vt</span><span class="o" style="font-weight: 600;">/</span><span class="nx">examples</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="nx">debian</span><span class="o" style="font-weight: 600;">/</span><span class="nx">tests</span><span class="o" style="font-weight: 600;">/</span><span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span> <span class="nx">usr</span><span class="o" style="font-weight: 600;">/</span><span class="nx">share</span><span class="o" style="font-weight: 600;">/</span><span class="nx">doc</span><span class="o" style="font-weight: 600;">/</span><span class="nx">vt</span></span></pre>
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<a href="https://salsa.debian.org/med-team/vt/-/compare/8d7a6047a9b5ecb846da38a0175ec394758eef8c...f73a688485e3cbfcb87d4d13ddcdfd9c247aee4b#9ef2917f6f883e279b64e7a65b915ab3d66f2e65"><strong>debian/vt.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 1.47.15.</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">.TH VT "1" "June 2020" "vt 0.57721+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">vt \- toolset for short variant discovery in genetic sequence data</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 vt</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"><tool> [options]</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">.SH TOOLS</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">view</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">view vcf/vcf.gz/bcf files</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">index</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">index vcf.gz/bcf files</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">normalize</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">normalize variants</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">decompose</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">decompose variants</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">uniq</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">drop duplicate variants</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">.TP</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">cat</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">concatenate VCF files</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">.TP</span>
</pre>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">paste</span>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">paste VCF files</span>
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30
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<pre style="margin: 0;">+<span id="LC30" 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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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">sort</span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">sort VCF files</span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">+<span id="LC33" 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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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">subset</span>
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35
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">subset VCF file to variants polymorphic in a sample</span>
</pre>
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36
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<pre style="margin: 0;">+<span id="LC36" 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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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">peek</span>
</pre>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">summary of variants in the vcf file</span>
</pre>
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39
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<pre style="margin: 0;">+<span id="LC39" 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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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">partition</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">partition variants</span>
</pre>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">.TP</span>
</pre>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">multi_partition</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">partition variants from multiple VCF files</span>
</pre>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.TP</span>
</pre>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">annotate_variants</span>
</pre>
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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="plaintext">annotate variants</span>
</pre>
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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="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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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">annotate_db_rsid</span>
</pre>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">annotate variants with dbSNP rsid</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">.TP</span>
</pre>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">annotate_1000g</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">annotate variants with 1000 Genomes variants</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">.TP</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">annotate_regions</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">annotate regions</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">.TP</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">compute_concordance</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">compute genotype concordance between 2 call sets</span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">.TP</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">compute_features</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">compute genotype likelihood based statistics</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">.TP</span>
</pre>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">discover</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">discover variants</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">.TP</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">genotype</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">genotype variants</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">.SH SEE ALSO</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">Help page on http://statgen.sph.umich.edu/wiki/Vt</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">.SH AUTHOR</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> This manpage was written by Andreas Tille for the Debian distribution and</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> can be used for any other usage of the program.</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">debian/README.test</span></pre>
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