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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/vcftools">Debian Med / vcftools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/431d28743c147ea6f50474dd687d23abb9174300">431d2874</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:01:04Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/57b74617112abaa7a77c89099a7872d5b18934c4">57b74617</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:09:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unneeded get-orig-source target
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/b363e3244d5e1b333b96fea76eefd2f3bee584a2">b363e324</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:13:30Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix interpreter line in Perl scripts
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/ca03f390f1cfca9d749d68f503d26111af73227b">ca03f390</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:20:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Part of the patch was lost in previous commit - restore
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/d9917b2fac6830ae6b08dc2e37c6f999b0023fc5">d9917b2f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:27:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix perl interpreter path
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/0a37831b2b04f5452b5e2c8bfaff10a0170fd9cb">0a37831b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:35:37Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix path also in examples
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/vcftools/commit/77a9019a7c4f1d7192f7cc3953aa8618d6d6bd83">77a9019a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-08-03T14:38:01Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#a79fed94e350acfae9268b420e4f5ffcee745d15">
debian/patches/manpage.patch
</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/vcftools/compare/689edd9ebcf278e67d44f8c469a20a9aed156dcc...77a9019a7c4f1d7192f7cc3953aa8618d6d6bd83#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num new_line old" data-linenumber="1" 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="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">vcftools (0.1.16-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">vcftools (0.1.16-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" 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="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream version dealing with CVE-2018-11099, CVE-2018-11129 and</span>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> CVE-2018-11130</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #902190</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="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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Point Vcs fields to salsa.debian.org</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="diff-line-num new_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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> * Standards-Version: 4.1.5</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Remove unneeded get-orig-source target</span>
</pre>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Fix interpreter line in Perl scripts</span>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 03 Aug 2018 1<span class="idiff left right">5:56:18</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Fri, 03 Aug 2018 1<span class="idiff left right">6:20:50</span> +0200</span>
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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">vcftools (0.1.15-1) unstable; urgency=medium</span>
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<td class="diff-line-num new_line" data-linenumber="14" 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="LC14" class="line" lang="plaintext"></span>
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<br>
</li>
<li id="a79fed94e350acfae9268b420e4f5ffcee745d15">
<a href="https://salsa.debian.org/med-team/vcftools/compare/689edd9ebcf278e67d44f8c469a20a9aed156dcc...77a9019a7c4f1d7192f7cc3953aa8618d6d6bd83#a79fed94e350acfae9268b420e4f5ffcee745d15"><strong>debian/patches/manpage.patch</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,10 +6,10 @@ Description: Fix manpage syntax</td>
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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/cpp/vcftools.1</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1,7 +1,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> .\" Manpage for vcftools.</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.TH vcftools man page 1 "<span class="idiff left right">05 January 2016" "0.1.14</span>" "vcftools man page"</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TH <span class="idiff left right">VCFTOOLS "1" "05 January 2017" "0.1.15</span>" "vcftools man page"</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-.TH vcftools man page 1 "<span class="idiff left right">2 August 2018" "0.1.16</span>" "vcftools man page"</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+.TH <span class="idiff left right">vcftools "1" "2 August 2018" "0.1.16</span>" "vcftools man page"</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> .SH NAME</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-vcftools v0.1.1<span class="idiff left right">4</span> \- Utilities for the variant call format (VCF) and binary variant call format (BCF)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-vcftools v0.1.1<span class="idiff left right">6</span> \- Utilities for the variant call format (VCF) and binary variant call format (BCF)</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+vcftools \- Utilities for the variant call format (VCF) and binary variant call format (BCF)</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> .SH SYNOPSIS</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> .B vcftools</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/vcftools/compare/689edd9ebcf278e67d44f8c469a20a9aed156dcc...77a9019a7c4f1d7192f7cc3953aa8618d6d6bd83#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,13 +16,15 @@ sampledir:=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/doc/$(DEB_SOURCE)/examples</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nl">override_dh_auto_configure</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"> dh_auto_configure <span class="nt" style="color: navy;">--</span> <span class="nt" style="color: navy;">--with-pmdir</span><span class="o" style="font-weight: 600;">=</span>/share/perl5</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="nl">override_dh_install</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> dh_install</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="make"> <span class="k" style="font-weight: 600;">for </span>perlscript <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-l</span> <span class="s1" style="color: #d14;">'#!/usr/bin/env \+perl'</span> debian/<span class="k" style="font-weight: 600;">*</span>/usr/bin/<span class="k" style="font-weight: 600;">*</span><span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'1s+#!/usr/bin/env perl+#!/usr/bin/perl+'</span> <span class="nv" style="color: teal;">$$</span><span class="o" style="font-weight: 600;">{</span>perlscript<span class="o" style="font-weight: 600;">}</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nl">override_dh_installchangelogs</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"> dh_installchangelogs src/perl/ChangeLog</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="make"><span class="nl">get-orig-source</span><span class="o" style="font-weight: 600;">:</span></span>
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23
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> ../tarballs</span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"> uscan <span class="nt" style="color: navy;">--verbose</span> <span class="nt" style="color: navy;">--force-download</span> <span class="nt" style="color: navy;">--repack</span> <span class="nt" style="color: navy;">--compression</span> xz <span class="nt" style="color: navy;">--destdir</span><span class="o" style="font-weight: 600;">=</span>../tarballs <span class="nt" style="color: navy;">--no-symlink</span></span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="make"></span>
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26
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="make"><span class="nl">override_dh_installexamples</span><span class="o" style="font-weight: 600;">:</span></span>
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27
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="make"> dh_installexamples<span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="make"> <span class="nb" style="color: #0086b3;">mkdir</span> <span class="nt" style="color: navy;">-p</span> <span class="nv" style="color: teal;">$(sampledir)</span>/testsuite<span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="32" 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="34" 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">@@ -32,3 +34,6 @@ override_dh_installexamples:</td>
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32
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'s#examples#testdata#g'</span> <span class="nv" style="color: teal;">$(sampledir)</span>/testsuite/test.t<span class="p">;</span></span>
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33
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'s#I\.\./perl/#I\.\./\.#g'</span> <span class="nv" style="color: teal;">$(sampledir)</span>/testsuite/test.t<span class="p">;</span></span>
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34
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'s#\.\./perl/#/usr/bin/#g'</span> <span class="nv" style="color: teal;">$(sampledir)</span>/testsuite/test.t<span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="make"> <span class="k" style="font-weight: 600;">for </span>perlscript <span class="k" style="font-weight: 600;">in</span> <span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">grep</span> <span class="nt" style="color: navy;">-lR</span> <span class="s1" style="color: #d14;">'#!/usr/bin/env \+perl'</span> debian/<span class="k" style="font-weight: 600;">*</span>/usr/share/doc/vcftools/examples<span class="sb" style="color: #d14;">`</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="make"> <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: navy;">-i</span> <span class="s1" style="color: #d14;">'1s+#!/usr/bin/env perl+#!/usr/bin/perl+'</span> <span class="nv" style="color: teal;">$$</span><span class="o" style="font-weight: 600;">{</span>perlscript<span class="o" style="font-weight: 600;">}</span> <span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="make"> <span class="k" style="font-weight: 600;">done</span></span></pre>
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