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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/htslib">Debian Med / htslib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/a1dcd61d85562f4dbf22695fa40464549c660054">a1dcd61d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-05T08:23:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing Depends: libcurl4-gnutls-dev, libdeflate-dev
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/9605bc10ef1a7cbdc51fc67aa949184662b270ab">9605bc10</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-05T08:34:47+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix run-unit-test script
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/7e0bf2deaf67d5e958398dbdf079d6cf1f8cb84b">7e0bf2de</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-05T08:35:06+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htslib/-/commit/d4320da3dc417dd1f33898105288a792c5fb28b0">d4320da3</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-05T08:48:19+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Debian has no libexecdir - plugins should go to libdir
</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="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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</li>
<li class="file-stats">
<a href="#141c83fa8dd51d2eeabad10acd632c5ec8c5fd41">
<span class="new-file">
+
debian/patches/plugins_to_lib.patch
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</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,9 @@ htslib (1.11-2) UNRELEASED; urgency=medium</td>
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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" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="mosel"></span>
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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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Enable</span> <span class="n" style="color: #333;">plugins</span></span>
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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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">Closes</span><span class="p">:</span> <span class="p">#</span><span class="m" style="color: #099;">971542</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">
5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Add</span> <span class="n" style="color: #333;">missing</span> <span class="n" style="color: #333;">Depends</span><span class="p">:</span> <span class="n" style="color: #333;">libcurl4</span><span class="p">-</span><span class="n" style="color: #333;">gnutls</span><span class="p">-</span><span class="n" style="color: #333;">dev</span><span class="p">,</span> <span class="n" style="color: #333;">libdeflate</span><span class="p">-</span><span class="n" style="color: #333;">dev</span></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="nf" style="color: #900; font-weight: 600;">run</span><span class="p">-</span><span class="n" style="color: #333;">unit</span><span class="p">-</span><span class="n" style="color: #333;">test</span> <span class="n" style="color: #333;">script</span></span>
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<td class="diff-line-num new new_line" data-linenumber="7" 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="LC7" class="line" lang="mosel"> <span class="p">*</span> <span class="n" style="color: #333;">Fix</span> <span class="n" style="color: #333;">autopkgtest</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="mosel"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="mosel"> <span class="p">--</span> <span class="n" style="color: #333;">Andreas</span> <span class="n" style="color: #333;">Tille</span> <span class="p"><</span><span class="n" style="color: #333;">tille</span><span class="p">@</span><span class="n" style="color: #333;">debian</span><span class="p">.</span><span class="n" style="color: #333;">org</span><span class="p">></span> <span class="n" style="color: #333;">Fri</span><span class="p">,</span> <span class="m" style="color: #099;">02</span> <span class="n" style="color: #333;">Oct</span> <span class="m" style="color: #099;">2020</span> <span class="m" style="color: #099;">11</span><span class="p">:</span><span class="m" style="color: #099;">35</span><span class="p">:</span><span class="m" style="color: #099;">21</span> <span class="p">+</span><span class="m" style="color: #099;">0200</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="mosel"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,6 +46,8 @@ Architecture: any</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Multi-Arch: same</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Depends: libhts3 (= ${binary:Version}),</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> libcurl4-gnutls-dev,</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> libdeflate-dev,</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> liblzma-dev,</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> zlib1g-dev,</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"> ${misc:Depends}</span>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#141c83fa8dd51d2eeabad10acd632c5ec8c5fd41"><strong>debian/patches/plugins_to_lib.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: Fri, 02 Oct 2020 11:35:21 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Debian has no libexecdir - plugins should go to libdir</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/configure.ac</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/configure.ac</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -115,11 +115,11 @@</span> AC_ARG_WITH([libdeflate],</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> AC_ARG_WITH([plugin-dir],</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> [AS_HELP_STRING([--with-plugin-dir=DIR],</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [plugin installation location [LIBEXECDIR/htslib]])],</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ [plugin installation location [LIBDIR/htslib]])],</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> [case $withval in</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> yes|no) MSG_ERROR([no directory specified for --with-plugin-dir]) ;;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> esac],</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- [with_plugin_dir='$(libexecdir)/htslib'])</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;">+ [with_plugin_dir='$(libdir)/htslib'])</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> AC_SUBST([plugindir], $with_plugin_dir)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> AC_ARG_WITH([plugin-path],</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -6,3 +6,4 @@ fix_float_precision</td>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"># big-endian</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">cram_to_bam_export.patch</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">273c5e76a1694aa2a13fd51c133abed2ef8ab4d3.patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">plugins_to_lib.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#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">@@ -83,6 +83,7 @@ override_dh_install-indep:</td>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"> dh_install --indep</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext"> sed -i 's/-ffile-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"> sed -i 's/-fdebug-prefix-map=[^[:space:]]* //g' debian/htslib-test/usr/share/htslib-test/config.mk</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> sed -i 's#\.\./\.\./htslib/hfile.h#htslib/hfile.h#' `grep -Rl '../../htslib/hfile.h' debian/htslib-test/*`</span>
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext">override_dh_installdocs:</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"> dh_installdocs</span>
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<a href="https://salsa.debian.org/med-team/htslib/-/compare/88644ba8e4096302d996dae2a0399195e2e53819...d4320da3dc417dd1f33898105288a792c5fb28b0#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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/bash</span></span>
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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</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;">pkg</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"htslib"</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="shell"></span>
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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="nv" style="color: #008080;">$AUTOPKGTEST_TMP</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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7
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<pre style="margin: 0;">-<span id="LC7" 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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<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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<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;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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9
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-aL</span> /usr/share/<span class="k" style="font-weight: 600;">${</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>/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$AUTOPKGTEST_TMP</span><span class="s2" style="color: #d14;">"</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +19,7 @@ sed -i 's#\$(HTSLIB)#/usr/include/#g' htslib.mk</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell"><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"-O2 -fno-strict-aliasing -fno-code-hoisting"</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">if </span><span class="nb" style="color: #0086b3;">grep </span>sse /proc/cpuinfo <span class="o" style="font-weight: 600;">></span> /dev/null<span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span>CFLAGS<span class="idiff left">+</span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"</span> -msse -mfpmath=sse"</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">CFLAGS</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">CFLAGS</span></span><span class="k" style="font-weight: 600;"><span class="idiff right">}</span></span><span class="s2" style="color: #d14;"> -msse -mfpmath=sse"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span>CFLAGS</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="shell"></span>
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