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<h3>
Nilesh Patra pushed to branch master
at <a href="https://salsa.debian.org/med-team/pftools">Debian Med / pftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/7d59f3fcbe3aaba97eb6b29f40beaff3ec157e88">7d59f3fc</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T07:38:29+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove man/* from debian/manpages
This is so because the CMakeLists.txt in man/ already seems to install
manpages at the right place.
Hence re-copying man/* leads to error
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/265814a17064523b816437730ecf9db638570ea1">265814a1</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T07:39:49+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove duplicate manpage (already present in man/)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/f11be1e5c985f95be4091bc4f01c8635a0103a3d">f11be1e5</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T07:42:12+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">dh_auto_clean Clean remaining stuff
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/1cb322c780593b1d47a99ae862d533b302536f86">1cb322c7</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T13:59:48+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove useless files, move docs to correct place
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/647a6b41510a277aa20214e2621e0b9734ac0bb7">647a6b41</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T14:00:08+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Really fix perl interpreter path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/pftools/-/commit/8288094a7701ca3cac4393eabb47807ce35f9532">8288094a</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-18T14:01:28+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update changelog
</pre>
</li>
</ul>
<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#68e0b13744e158347bfd74ebaaca667435f07d14">
debian/manpages
</a>
</li>
<li class="file-stats">
<a href="#83da178741ee9770c8434f85e0d222f70d0d7713">
debian/patches/fix_perl_interpreter.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#2a8c8251da515b2d221f652d78826c7f449247d7">
<span class="deleted-file">
−
debian/pfsearch.1
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">pftools (3.2.6-1) UNRELEASED; urgency=medium</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="3" 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="LC4" class="line" lang="plaintext"> * Fix gcc-10 FTBFS</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="5" 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="3" 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="LC5" class="line" lang="plaintext"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team Upload.</span>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Fix watch file and homepage</span>
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<td class="diff-line-num old_line" data-linenumber="8" 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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,7 +17,14 @@ pftools (3.2.6-1) UNRELEASED; urgency=medium</td>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> * Force sequential execution of tests</span>
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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> * No need to replace [gh]top any more in examples</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 24 Nov 2020 21:17:21 +0100</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> [ Nilesh Patra ]</span>
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> * Remove man/* from debian/manpages</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" 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="LC22" class="line" lang="plaintext"> * Remove duplicate manpage (already present in man/)</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> * dh_auto_clean Clean remaining stuff</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> * Remove useless files, move docs to correct place</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="plaintext"> * Really fix perl interpreter path</span>
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<td class="diff-line-num new old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> -- Nilesh Patra <npatra974@gmail.com> Fri, 18 Dec 2020 14:00:23 +0530</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">pftools (3+dfsg-3) unstable; urgency=medium</span>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#68e0b13744e158347bfd74ebaaca667435f07d14"><strong>debian/manpages</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># man/*</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/*.1</span></pre>
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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/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#83da178741ee9770c8434f85e0d222f70d0d7713"><strong>debian/patches/fix_perl_interpreter.patch</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: <span class="idiff left right">Tue, 24 Nov 2020 21:17:21 +010</span>0</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org><span class="idiff left right">, Nilesh Patra <npatra974@gmail.com></span></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: <span class="idiff left right">Fri, 18 Dec 2020 13:33:50 +053</span>0</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Description: Fix interpreter of perl script to fix build time test</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/src/Perl/sort_fasta.pl</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/sort_fasta.pl</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> use strict;</span>
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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">@@ -13,8 +13,64 @@ Description: Fix interpreter of perl script to fix build time test</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/make_iupac_cmp.pl</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/make_iupac_cmp.pl</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/<span class="idiff left right">usr/</span>bin/env perl</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> use strict;</span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> use Getopt::Std;</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/compare_2_profiles.pl</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/compare_2_profiles.pl</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> # Perl embedded modules</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/ps_scan.pl</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/ps_scan.pl</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> # ps_scan - a PROSITE scanning program</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/scramble_fasta.pl</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/scramble_fasta.pl</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> use strict;</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/split_profile_file.pl</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/split_profile_file.pl</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> # Perl embedded modules</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Perl/fasta_to_fastq.pl</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Perl/fasta_to_fastq.pl</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> #Copyright (c) 2010 LUQMAN HAKIM BIN ABDUL HADI (csilhah@nus.edu.sg)</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> #</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> #Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_pfsearchV3_iupac.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_pfsearchV3_iupac.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/examples/test_scan_search.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/examples/test_scan_search.pl.cmake</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env perl</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/perl</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> use strict;</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">spelling.patch</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># fix_perl_interpreter.patch</span>
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3
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">0001-Harmonize-bin-env-path-Cleaning.patch</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fix_perl_interpreter.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">destdir_for_examples.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#2a8c8251da515b2d221f652d78826c7f449247d7"><strong>debian/pfsearch.1</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">.TH PFSEARCH "1" "March 2017" "pfsearch 3" "User Commands"</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">.SH NAME</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">pfsearch \- search protein and DNA generalized profiles (legacy)</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">.SH SYNOPSIS</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">.B pfsearch</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">[ \fI\,-abCdfhlLmMkrsuvWxyz \/\fR] [ \fI\,profile-file | - \/\fR] [ \fI\,seq-library-file | - \/\fR] [ \fI\,parameters \/\fR]</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">.SH DESCRIPTION</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">Build protein and DNA generalized profiles and use them to scan and align sequences,</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">and search databases.</span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">.SH OPTIONS</span>
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11
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">\fB\-a\fR: report optimal alignment for all sequences.</span>
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<td class="diff-line-num old old_line" data-linenumber="13" 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">
13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="14" 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">
14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">\fB\-b\fR: search complementary strand of DNA sequences.</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">\fB\-f\fR: input sequence file is in FASTA format.</span>
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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">\fB\-h\fR: print usage help text.</span>
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<td class="diff-line-num old old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="20" 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">
20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">\fB\-l\fR: indicate highest cut\-off level (number).</span>
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<td class="diff-line-num old old_line" data-linenumber="21" 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">
21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="22" 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">
22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">\fB\-L\fR: indicate highest cut\-off level (text).</span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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">
23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="24" 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">
24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">\fB\-m\fR: report individual matches for circular profiles.</span>
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<td class="diff-line-num old old_line" data-linenumber="25" 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">
25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="26" 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">
26
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">\fB\-r\fR: use raw score.</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">\fB\-u\fR: force profile disjointness to UNIQUE.</span>
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<td class="diff-line-num old old_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">.HP</span>
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<td class="diff-line-num old old_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">\fB\-C\fR<value>:</span>
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<td class="diff-line-num old old_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num old old_line" data-linenumber="32" 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">
32
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">cut\-off value. An integer value forces \fB\-r\fR. Same as parameter C.</span>
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<td class="diff-line-num old old_line" data-linenumber="33" 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">
33
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">.HP</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">\fB\-M\fR<value>:</span>
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35
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">.IP</span>
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36
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">set the normalization mode to use for the score computation.</span>
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37
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">Overrides the profile PRIORITY parameter.</span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext">.IP</span>
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39
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">output modifiers:</span>
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40
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext">.HP</span>
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41
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">\fB\-d\fR: impose length limit on sequence description.</span>
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42
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext">.HP</span>
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43
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">\fB\-k\fR: output using the xPSA header (using keyword=value pairs).</span>
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44
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext">.HP</span>
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45
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">\fB\-s\fR: list sequences of the matched regions.</span>
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46
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">.HP</span>
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47
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext">\fB\-v\fR: suppress warnings on stderr.</span>
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48
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">.HP</span>
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49
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext">\fB\-x\fR: list alignments in PSA format.</span>
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50
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">.HP</span>
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51
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext">\fB\-y\fR: list alignments in human readable form.</span>
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52
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext">.HP</span>
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53
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext">\fB\-z\fR: indicate profile start and stop positions.</span>
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54
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">.HP</span>
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55
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">\fB\-W\fR<value>:</span>
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56
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num old old_line" data-linenumber="57" 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">
57
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="plaintext">specifies the output width. Same as parameter W.</span>
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<td class="diff-line-num old old_line" data-linenumber="58" 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">
58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">.IP</span>
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<td class="diff-line-num old old_line" data-linenumber="59" 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">
59
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="plaintext">valid (but deprecated) parameters are:</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">[C=cut\-off\-value]</span>
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62
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">use option \fB\-C\fR instead</span>
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63
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">.TP</span>
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64
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">[W=output\-width]</span>
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65
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="plaintext">use option \fB\-W\fR instead</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">.SH AUTHOR</span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="plaintext">This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.</span></pre>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/pftools/-/compare/926e3a358ffb268aa8f5c6b41fd75d8e5fdb32d3...8288094a7701ca3cac4393eabb47807ce35f9532#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,6 +21,8 @@ override_dh_installman:</td>
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21
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> dh_installman</span>
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/share/man/man1/gtop.1 debian/$(DEB_SOURCE)/usr/share/man/man1/pfgtop.1</span>
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/share/man/man1/htop.1 debian/$(DEB_SOURCE)/usr/share/man/man1/pfhtop.1</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> mv debian/$(DEB_SOURCE)/usr/share/doc/*.pdf debian/$(DEB_SOURCE)/usr/share/doc/${DEB_SOURCE}/</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> rm -f debian/$(DEB_SOURCE)/usr/share/doc/*.txt debian/${DEB_SOURCE}/usr/ChangeLog debian/${DEB_SOURCE}/usr/README* debian/${DEB_SOURCE}/usr/LICENSE</span>
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24
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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25
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -34,3 +36,7 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</td>
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34
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> grep -v '^DT *' test.out > test.compare ; \</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> diff -u test.compare test.build || true</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext">endif</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> rm -rf data/test.*</span></pre>
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