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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/4d480293f495e5dc9425ee6c0ee3377d31878607">4d480293</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-12-24T15:23:01+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.30.2</pre>
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<h4>6 changed files:</h4>
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<li class="file-stats">
<a href="#fe77d5d1439f26e353a42bbd38dece2467ff6558">
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+
.github/workflows/build.yml
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<li class="file-stats">
<a href="#6cd2a502257ede524d220cea6700e2fa98f071aa">
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+
.github/workflows/wheels.yml
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<li class="file-stats">
<a href="#2fbcc692367300b0691462028f2e5f9bcaaf0945">
cyvcf2/__init__.py
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<li class="file-stats">
<a href="#164dc8610052ecd4fe73493df7bd8d4346cc2aa4">
cyvcf2/cyvcf2.pyx
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<li class="file-stats">
<a href="#28f51c3e09bca3c80d5e6f86d940cac251d75400">
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cyvcf2/tests/test-invalid-header.vcf
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<li class="file-stats">
<a href="#fd11e2e4bd1b8903c21cf95e681058bd017b76b9">
cyvcf2/tests/test_reader.py
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<h4>Changes:</h4>
<li id="fe77d5d1439f26e353a42bbd38dece2467ff6558">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/4d480293f495e5dc9425ee6c0ee3377d31878607#fe77d5d1439f26e353a42bbd38dece2467ff6558"><strong>.github/workflows/build.yml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="3" 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="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">push</span><span class="pi">,</span> <span class="nv" style="color: #008080;">pull_request</span><span class="pi">]</span></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">
4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</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">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="na" style="color: #008080;">build</span><span class="pi">:</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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run tests on Python ${{ matrix.python-version }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" 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">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-18.04</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" 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">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="10" 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">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" 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="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">3.5</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.6</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.7</span><span class="pi">,</span> <span class="nv" style="color: #008080;">3.8</span><span class="pi">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="12" 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="LC12" class="line" lang="yaml"></span>
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<td class="diff-line-num new new_line" data-linenumber="13" 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="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="14" 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="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="15" 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="LC15" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="16" 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="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">submodules</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up Python ${{ matrix.python-version }}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.python-version }}</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="s" style="color: #d14;">sudo apt-get install libcurl4-openssl-dev</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="s" style="color: #d14;">pip install -r requirements.txt</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd htslib</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="s" style="color: #d14;">autoheader && autoconf</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">./configure --enable-s3 --disable-lzma --disable-bz2</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="s" style="color: #d14;">make</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="s" style="color: #d14;">cd ..</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="s" style="color: #d14;">CYTHONIZE=1 python setup.py install</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Test</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="s" style="color: #d14;">python setup.py test</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/4d480293f495e5dc9425ee6c0ee3377d31878607#6cd2a502257ede524d220cea6700e2fa98f071aa"><strong>.github/workflows/wheels.yml</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Wheels</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">on</span><span class="pi">:</span> </span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="yaml"> <span class="na" style="color: #008080;">push</span><span class="pi">:</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="yaml"> <span class="na" style="color: #008080;">tags</span><span class="pi">:</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml"> <span class="pi">-</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">v*.*.*'</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml"></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">jobs</span><span class="pi">:</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">build_wheels</span><span class="pi">:</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build wheels on ${{ matrix.os }}</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">${{ matrix.os }}</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml"> <span class="na" style="color: #008080;">strategy</span><span class="pi">:</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml"> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="pi">[</span><span class="nv" style="color: #008080;">ubuntu-18.04</span><span class="pi">,</span> <span class="nv" style="color: #008080;">macos-latest</span><span class="pi">]</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml"></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="na" style="color: #008080;">steps</span><span class="pi">:</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">submodules</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/setup-python@v2</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install Python</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">python-version</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Install cibuildwheel</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m pip install cibuildwheel</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build wheels for Linux</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">matrix.os == 'ubuntu-18.04'</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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32
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m cibuildwheel --output-dir wheelhouse</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_SKIP</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pp*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cp27-*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cp34-*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">*i686*"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_MANYLINUX_X86_64_IMAGE</span><span class="pi">:</span> <span class="s" style="color: #d14;">manylinux2014</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_BEFORE_BUILD_LINUX</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">{project}/ci/linux-deps"</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_TEST_COMMAND</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">{project}/ci/test"</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_ENVIRONMENT</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">CYTHONIZE=1</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">LDFLAGS='-L/usr/lib64/openssl11'</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CPPFLAGS='-I/usr/include/openssl11'</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">C_INCLUDE_PATH='/root/include'</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">LIBRARY_PATH='/root/lib'"</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="yaml"></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Build wheels for Mac OS</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">matrix.os == 'macos-latest'</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="yaml"> <span class="na" style="color: #008080;">run</span><span class="pi">:</span> <span class="pi">|</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="yaml"> <span class="s" style="color: #d14;">python -m cibuildwheel --output-dir wheelhouse</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_SKIP</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">pp*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cp27-*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">cp34-*</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">*i686*"</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_MANYLINUX_X86_64_IMAGE</span><span class="pi">:</span> <span class="s" style="color: #d14;">manylinux2014</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_BEFORE_BUILD_MACOS</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">{project}/ci/osx-deps"</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_TEST_COMMAND</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">{project}/ci/test"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">CIBW_ENVIRONMENT</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">CYTHONIZE=1"</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="na" style="color: #008080;">LDFLAGS</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">-L/usr/local/opt/openssl@1.1/lib"</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="na" style="color: #008080;">CPPFLAGS</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">-I/usr/local/opt/openssl@1.1/include"</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="yaml"> <span class="na" style="color: #008080;">PKG_CONFIG_PATH</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">/usr/local/opt/openssl@1.1/lib/pkgconfig"</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="yaml"></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/upload-artifact@v2</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="na" style="color: #008080;">path</span><span class="pi">:</span> <span class="s" style="color: #d14;">./wheelhouse/*.whl</span></span></pre>
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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">@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="n" style="color: #333;">par_het</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCFReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.<span class="idiff left right">1</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.<span class="idiff left right">2</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/4d480293f495e5dc9425ee6c0ee3377d31878607#164dc8610052ecd4fe73493df7bd8d4346cc2aa4"><strong>cyvcf2/cyvcf2.pyx</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">@@ -256,6 +256,8 @@ cdef class VCF(HTSFile):</td>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">bcf_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hdr</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_open_htsfile</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cython"> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_read</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hdr</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">Exception</span><span class="p">(</span><span class="s" style="color: #d14;">"cannot parse VCF header"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">samples</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">set_samples</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_nsamples</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">##fileformat=VCFv4.0</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT FOO </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">20 10001292 rs1 G A 42.22 . AF=0.50;AC=1 GT:RD:GQ 1/0:23:19.28</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">20 10002963 . C G 42.22 . AF=0.30 GT:RD:GQ 0/1:30:33.07</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">20 10005008 rs2 A T 123.78 . AF=1.00 GT:RD:GQ 1/1:30:8.26</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">20 10044557 rs3 C T 42.22 . AC=2 GT:RD:GQ 0/1:31:15.01</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">20 10048580 . T A 42.22 . AF=0.75 GT:RD:GQ 1/0:33:23.49</span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/4d480293f495e5dc9425ee6c0ee3377d31878607#fd11e2e4bd1b8903c21cf95e681058bd017b76b9"><strong>cyvcf2/tests/test_reader.py</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1138" 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="1138" 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">@@ -1138,3 +1138,9 @@ def test_set_unknown_format():</td>
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1138
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1138
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<pre style="margin: 0;"> <span id="LC1138" class="line" lang="python"> <span class="n" style="color: #333;">parts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>
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1139
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1139
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<pre style="margin: 0;"> <span id="LC1139" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'.'</span></span>
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1140
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1140
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<pre style="margin: 0;"> <span id="LC1140" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">parts</span><span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">3</span><span class="p">:]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'1.1'</span></span>
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1141
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<pre style="margin: 0;">+<span id="LC1141" class="line" lang="python"></span>
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1142
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<pre style="margin: 0;">+<span id="LC1142" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_invalid_header</span><span class="p">():</span></span>
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1143
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<pre style="margin: 0;">+<span id="LC1143" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># htslib produces the error "Empty sample name: trailing spaces/tabs in the header line?"</span></span>
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1144
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<pre style="margin: 0;">+<span id="LC1144" class="line" lang="python"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">HERE</span><span class="p">,</span> <span class="s" style="color: #d14;">"test-invalid-header.vcf"</span><span class="p">)</span></span>
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1145
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<pre style="margin: 0;">+<span id="LC1145" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>
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1146
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<pre style="margin: 0;">+<span id="LC1146" class="line" lang="python"> <span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">,</span> <span class="n" style="color: #333;">VCF</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">)</span></span></pre>
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