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<h3>
Pranav Ballaney pushed to branch master
at <a href="https://salsa.debian.org/med-team/sniffles">Debian Med / sniffles</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/e0a521474b246c376d52da519c76d394b497675d">e0a52147</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T06:00:15+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix INCLUDE_PATHS. Closes: #963299.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/e8a8d3db4b59ef529a3f335227c4a285f647807b">e8a8d3db</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T06:06:05+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add to Uploaders
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/sniffles/-/commit/8ce66c5cd09c8b955f6144e3ea7215b37ea631fe">8ce66c5c</a></strong>
<div>
<span>by Pranav Ballaney</span>
<i>at 2020-07-03T06:06:20+05:30</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install examples and docs
</pre>
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<h4>8 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
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+
debian/README.test
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</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32">
debian/docs
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<li class="file-stats">
<a href="#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c">
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+
debian/examples
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
debian/tests/control
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="f6a99a1e522a0f5ca122fd9818a9d8536ea59942">
<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#f6a99a1e522a0f5ca122fd9818a9d8536ea59942"><strong>debian/README.test</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="nx">Notes</span> <span class="nx">on</span> <span class="nx">how</span> <span class="nx">this</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span><span class="o" style="font-weight: 600;">.</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="err" style="color: #a61717; background-color: #e3d2d2;">────────────────────────────────────────</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"></span>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="nx">This</span> <span class="nx">package</span> <span class="nx">can</span> <span class="nx">be</span> <span class="nx">tested</span> <span class="nx">by</span> <span class="nx">running</span> <span class="nx">the</span> <span class="nx">provided</span> <span class="nx">test</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"></span>
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<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="php"> <span class="nx">sh</span> <span class="nx">run</span><span class="o" style="font-weight: 600;">-</span><span class="nx">unit</span><span class="o" style="font-weight: 600;">-</span><span class="nx">test</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="php"><span class="nx">in</span> <span class="nx">order</span> <span class="nx">to</span> <span class="nx">confirm</span> <span class="nx">its</span> <span class="nx">integrity</span><span class="o" style="font-weight: 600;">.</span></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">sniffles (1.0.11+ds-1ubuntu1) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Afif Elghraoui ]</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Remove myself from Uploaders</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> [ Steffen Moeller ]</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="plaintext"> * d/u/metadata: yamllint</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> [ Steffen Möller ]</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Update metadata with ref to conda</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * Update metadata / added ref to bio.tools</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> [ Pranav Ballaney ]</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> * Fix INCLUDE_PATHS. Closes: #963299.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> * Add to Uploaders</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> * Install examples and docs</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> -- Pranav Ballaney <ballaneypranav@gmail.com> Fri, 03 Jul 2020 06:02:36 +0530</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="LC20" class="line" lang="plaintext">sniffles (1.0.11+ds-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> * Team upload.</span>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Source: sniffles</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Pranav Ballaney <ballaneypranav@gmail.com></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: science</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 12~),</span>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#3a5a7cdb36d3ebf45777d0bc382dd46aa7a18f32"><strong>debian/docs</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">README.md</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">debian/README*</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#9a14945e16c9144bd18a7ed182b1f8e4a2b50d7c"><strong>debian/examples</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">test_set/*</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#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">@@ -4,17 +4,14 @@</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">export DEB_BUILD_MAINT_OPTIONS = hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">INCLUDE_PATHS = /usr/include/bamtools</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">space=</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">space+=</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">INCLUDE_PATHS=/usr/include/bamtools</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@</span>
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14
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">override_dh_auto_configure:</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> dh_auto_configure -- \</span>
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17
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> -DCMAKE_INCLUDE_PATH="$<span class="idiff left right">(subst $(space),:,$(strip $(INCLUDE_PATHS)))</span>"</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> -DCMAKE_INCLUDE_PATH="$<span class="idiff left right">{INCLUDE_PATHS}</span>"</span>
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18
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_clean:</span>
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20
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_auto_clean</span>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Test-Command:</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"> sniffles -m test_set/reads_region.bam -v ${AUTOPKGTEST_TMP}/test.vcf;</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Restrictions: allow-stderr</span></pre>
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<a href="https://salsa.debian.org/med-team/sniffles/-/compare/7d9af156d348796e5a694097750d887e19a7f536...8ce66c5cd09c8b955f6144e3ea7215b37ea631fe#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#!/bin/bash</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>sniffles</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># Double quote below to expand the temporary directory variable now versus</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># later is on purpose.</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"> <span class="c" style="color: #998; font-style: italic;"># shellcheck disable=SC2064</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/examples/<span class="k" style="font-weight: 600;">*</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;">#do_stuff_to_test_package#</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell">sniffles <span class="nt" style="color: #000080;">-m</span> reads_region.bam <span class="nt" style="color: #000080;">-v</span> test.vcf</span></pre>
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