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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/python-pyvcf">Debian Med / python-pyvcf</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/4030f0faeff55558916e519d4dd525d0e7f72903">4030f0fa</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-09T08:08:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Breaks+Replaces: python3-pyvcf
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/587b437d8188e9b8510b46040830a5524f76aa95">587b437d</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-09T09:41:46Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Run Build-Time test, add autopkgtest
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/f0bf1db17b8a826a586bfbc30ef51c1df870b66d">f0bf1db1</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-09T09:43:59Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Depends: python3-pysam
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/d4e460ccb2a5a8e832cb08ed2126bf2fbc4a57dc">d4e460cc</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-12-09T09:44:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix dependency for pyvcf package
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/7714f2c877584cb8331fd392ecb3d99e3a52ffe1">7714f2c8</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-09T10:12:26Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not unzip originally gzipped files, It turned out that re-gzipping after unzipping will break the test!
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/python-pyvcf/commit/4d681337bab4672bc4d832d8a4359f8296100e57">4d681337</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-09T10:15:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<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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<a href="#83223a554d33ba7e1888274ff8ac43adb8147ba0">
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+
debian/tests/control
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<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
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+
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">python-pyvcf (0.6.8+git20170215.476169c-<span class="idiff left right">4) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">python-pyvcf (0.6.8+git20170215.476169c-<span class="idiff left right">5) unstable</span>; 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"> TODO: Reupload with source-only upload</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> Craft real test based on code snippets in README.rst</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Breaks+Replaces: python3-pyvcf</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Closes: #946427</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Run Build-Time test</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Add autopkgtest</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Depends: python3-pysam</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> * Fix dependency for pyvcf package</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="LC6" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Fri, 29 Nov 2019 13:02:31</span> +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Mon, 09 Dec 2019 11:12:54</span> +0100</span>
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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">python-pyvcf (0.6.8+git20170215.476169c-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -8,7 +8,9 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> cython3,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-all-dev,</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> python3-setuptools</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> python3-pytest <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> python3-pysam <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.4.1</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git</span>
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<td class="diff-line-num unfold js-unfold old_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">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +20,11 @@ Package: python3-vcf</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> ${python3:Depends}</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-pysam</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">Breaks: python3-pyvcf</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">Provides: python3-pyvcf</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Replaces: python3-pyvcf</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">Description: Variant Call Format (VCF) parser for Python 3</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"> The Variant Call Format (VCF) specifies the format of a text file used</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> in bioinformatics for storing gene sequence variations. The format has</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">@@ -40,7 +46,7 @@ Package: pyvcf</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Depends: ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"> ${python3:Depends},</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> python3-<span class="idiff left right">py</span>vcf</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> python3-vcf</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Description: helper scripts for Variant Call Format (VCF) parser</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"> The Variant Call Format (VCF) specifies the format of a text file used</span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"> in bioinformatics for storing gene sequence variations. The format has</span>
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<a href="https://salsa.debian.org/med-team/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57#83223a554d33ba7e1888274ff8ac43adb8147ba0"><strong>debian/tests/control</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Tests: run-unit-test</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Depends: @</span>
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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/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57#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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-e</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="shell"></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>python3-vcf</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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: #008080;">LC_ALL</span><span class="o" style="font-weight: 600;">=</span>C.UTF-8</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: #000080;">-x</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mkdir</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>/vcf</span>
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14
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<pre style="margin: 0;">+<span id="LC14" 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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</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>/vcf</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="s2" style="color: #d14;">"</span><span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">AUTOPKGTEST_TMP</span><span class="k" style="font-weight: 600;">}</span><span class="s2" style="color: #d14;">"</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell"></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># Do not unzip originally gzipped files</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># It turned out that re-gzipping after unzipping will break the test!</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="shell"><span class="nv" style="color: #008080;">NO_UNZIP_DIR</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</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;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="shell"><span class="k" style="font-weight: 600;">for </span>gz <span class="k" style="font-weight: 600;">in </span>1kg.vcf.gz issue-201.vcf.gz tb.vcf.gz <span class="p">;</span> <span class="k" style="font-weight: 600;">do</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nb" style="color: #0086b3;">mv </span>vcf/test/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">gz</span><span class="k" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NO_UNZIP_DIR</span><span class="k" style="font-weight: 600;">}</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="shell"><span class="k" style="font-weight: 600;">done</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: #000080;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="shell"><span class="nb" style="color: #0086b3;">mv</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NO_UNZIP_DIR</span><span class="k" style="font-weight: 600;">}</span>/<span class="k" style="font-weight: 600;">*</span> vcf/test</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="shell"><span class="nb" style="color: #0086b3;">rmdir</span> <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">NO_UNZIP_DIR</span><span class="k" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="shell">pytest-3</span></pre>
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