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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/09dacf19d9e0e0bfd2c60d38d1141c31106cffff">09dacf19</a></strong>
<div>
<span>by Nilesh Patra</span>
<i>at 2020-07-09T22:36:55+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.20.1</pre>
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<h4>10 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#2fbcc692367300b0691462028f2e5f9bcaaf0945">
cyvcf2/__init__.py
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<li class="file-stats">
<a href="#d7ed01d76169bd47314f52e31c36d1d22cf6812d">
cyvcf2/cyvcf2.pxd
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<li class="file-stats">
<a href="#164dc8610052ecd4fe73493df7bd8d4346cc2aa4">
cyvcf2/cyvcf2.pyx
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<li class="file-stats">
<a href="#fd11e2e4bd1b8903c21cf95e681058bd017b76b9">
cyvcf2/tests/test_reader.py
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<li class="file-stats">
<a href="#aded7756cdea7c289134466a0d54da4f26d43abb">
docs/source/conf.py
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<li class="file-stats">
<a href="#62df078594b947ca6f787a59ae6ddefabce9fcad">
docs/source/index.rst
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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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>
<td class="diff-line-num unfold js-unfold new_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>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,3 +18,4 @@ _static</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">_templates</span>
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<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">setup-requires/*</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">.cache/v/cache/lastfailed</span>
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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" 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="LC21" class="line" lang="plaintext">.idea</span></pre>
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<br>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" 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="15" 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">@@ -15,7 +15,7 @@ install:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">./configure --enable-s3 --disable-lzma --disable-bz2</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd ..</span></span>
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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py install</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;"><span class="idiff left right">CYTHONIZE=1 </span>python setup.py install</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">python setup.py test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">cyvcf2</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">Note: cyvcf2 versions <span class="nt" style="color: #000080;"><</span> <span class="nt" style="color: #000080;">0</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">20</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">0</span> <span class="na" style="color: #008080;">require</span> <span class="na" style="color: #008080;">htslib</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;"><</span> <span class="na" style="color: #008080;">1</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span><span class="na" style="color: #008080;">10</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">.</span> <span class="na" style="color: #008080;">cyvcf2</span> <span class="na" style="color: #008080;">versions</span> <span class="nt" style="color: #000080;">></span>= 0.20.0 require htslib >= 1.10</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="c" style="color: #998; font-style: italic;"><!-- ghp-import -p docs/build/html/ --></span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docs</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/docs-latest-blue.svg</span><span class="p">)</span>](http://brentp.github.io/cyvcf2/)</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></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">@@ -9,7 +11,7 @@ If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformati</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown">Fast python <span class="gs" style="font-weight: 600;">**(2 and 3)**</span> parsing of VCF and BCF including region-queries.</span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">org/brentp/cyvcf2.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org</span>/brentp/cyvcf2)</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.<span class="idiff left">com/brentp/cyvcf2.svg?branch=master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.com</span>/brentp/cyvcf2)</span>
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13
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"></span>
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14
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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown">cyvcf2 is a cython wrapper around <span class="p">[</span><span class="nv" style="color: #008080;">htslib</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/samtools/htslib</span><span class="p">)</span> built for fast parsing of <span class="p">[</span><span class="nv" style="color: #008080;">Variant Call Format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://en.m.wikipedia.org/wiki/Variant_Call_Format</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">VCF</span><span class="p">)</span> files.</span>
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15
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></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">@@ -68,7 +70,7 @@ for v in vcf('11:435345-556565'):</td>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Installation</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">============</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## pip</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## pip<span class="idiff left right"> (assuming you have htslib < 1.10 installed)</span></span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown">pip install cyvcf2</span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,7 +86,7 @@ autoconf</td>
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84
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown">make</span>
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85
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">cd ..</span>
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87
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown">pip install -e .</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="idiff left right">CYTHONIZE=1 </span>pip install -e .</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">On <span class="gs" style="font-weight: 600;">**OSX**</span>, using brew, you may have to set the following as indicated by the brew install:</span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#2fbcc692367300b0691462028f2e5f9bcaaf0945"><strong>cyvcf2/__init__.py</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">@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,</td>
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2
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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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3
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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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4
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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.<span class="idiff left right">11.6</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.<span class="idiff left right">20.1</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#d7ed01d76169bd47314f52e31c36d1d22cf6812d"><strong>cyvcf2/cyvcf2.pxd</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">libc.stdint</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">int32_t</span><span class="p">,</span> <span class="n" style="color: #333;">uint32_t</span><span class="p">,</span> <span class="n" style="color: #333;">int8_t</span><span class="p">,</span> <span class="n" style="color: #333;">int16_t</span><span class="p">,</span> <span class="n" style="color: #333;">uint8_t</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">libc.stdint</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">int<span class="idiff left">64_t</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">int</span>32_t</span><span class="p">,</span> <span class="n" style="color: #333;">uint32_t</span><span class="p">,</span> <span class="n" style="color: #333;">int8_t</span><span class="p">,</span> <span class="n" style="color: #333;">int16_t</span><span class="p">,</span> <span class="n" style="color: #333;">uint8_t</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cython"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cython"><span class="kn" style="font-weight: 600;">cimport</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cython"><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">import_array</span><span class="p">()</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,7 +23,7 @@ cdef extern from "htslib/kstring.h":</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cython"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">inline</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ks_release</span><span class="p">(</span><span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">ks_release</span><span class="p">(</span><span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">extern</span> <span class="k" style="font-weight: 600;">from</span> <span class="s" style="color: #d14;">"htslib/hfile.h"</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="cython"> <span class="k" style="font-weight: 600;">ctypedef</span> <span class="kr" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">hFILE</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="79" 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">@@ -79,7 +79,7 @@ cdef extern from "htslib/tbx.h":</td>
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cython"></span>
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80
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cython"> <span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">tbx_index_load</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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81
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81
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cython"> <span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">tbx_index_load2</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fnidx</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cython"> <span class="n" style="color: #333;">hts_itr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">tbx_itr_queryi</span><span class="p">(</span><span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tbx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">beg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">in</span>t</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cython"> <span class="n" style="color: #333;">hts_itr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">tbx_itr_queryi</span><span class="p">(</span><span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tbx</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int<span class="idiff left">64_t</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">beg</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff right">int64_</span>t</span> <span class="n" style="color: #333;">end</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cython"> <span class="n" style="color: #333;">hts_itr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">tbx_itr_querys</span><span class="p">(</span><span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tbx</span><span class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">reg</span><span class="p">)</span> <span class="k" style="font-weight: 600;">nogil</span></span>
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84
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">tbx_itr_next</span><span class="p">(</span><span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tbx</span><span class="p">,</span> <span class="n" style="color: #333;">hts_itr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">iter</span><span class="p">,</span> <span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">)</span> <span class="k" style="font-weight: 600;">nogil</span><span class="p">;</span></span>
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85
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cython"> <span class="n" style="color: #333;">void</span> <span class="nf" style="color: #900; font-weight: 600;">tbx_destroy</span><span class="p">(</span><span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tbx</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="109" 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="109" 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">@@ -109,8 +109,6 @@ cdef extern from "htslib/vcf.h":</td>
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cython"> <span class="n" style="color: #333;">const</span> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">BCF_BT_FLOAT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span></span>
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110
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cython"> <span class="n" style="color: #333;">const</span> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">BCF_BT_CHAR</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">7</span></span>
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111
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111
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<pre style="margin: 0;"> <span id="LC111" class="line" lang="cython"></span>
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112
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<pre style="margin: 0;">-<span id="LC112" class="line" lang="cython"> <span class="n" style="color: #333;">const</span> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">BCF_HT_FLAG</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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113
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<pre style="margin: 0;">-<span id="LC113" class="line" lang="cython"></span>
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114
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cython"> <span class="n" style="color: #333;">const</span> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">bcf_str_missing</span> <span class="o" style="font-weight: 600;">=</span> <span class="mh" style="color: #099;">0x07</span></span>
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115
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cython"> <span class="n" style="color: #333;">const</span> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">bcf_str_vector_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cython"></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">@@ -139,13 +137,14 @@ cdef extern from "htslib/vcf.h":</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cython"> <span class="k" style="font-weight: 600;">ctypedef</span> <span class="kr" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">bcf_info_t</span><span class="p">:</span></span>
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141
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">key</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># key: numeric tag id, the corresponding string is bcf_hdr_t::id[BCF_DT_ID][$key].key</span></span>
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142
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nb" style="color: #0086b3;">type</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">len</span></span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># type: one of BCF_BT_* types; len: vector length, 1 for scalars</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># type: one of BCF_BT_* types; len: vector length, 1 for scalars</span></span>
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143
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#} v1; # only set if $len==1; for easier access</span></span>
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144
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="cython"> <span class="n" style="color: #333;">uv1</span> <span class="n" style="color: #333;">v1</span></span>
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145
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="cython"> <span class="n" style="color: #333;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">vptr</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># pointer to data array in bcf1_t->shared.s, excluding the size+type and tag id bytes</span></span>
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146
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<pre style="margin: 0;"> <span id="LC144" class="line" lang="cython"> <span class="n" style="color: #333;">uint32_t</span> <span class="n" style="color: #333;">vptr_len</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># length of the vptr block or, when set, of the vptr_mod block, excluding offset</span></span>
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<pre style="margin: 0;"> <span id="LC145" class="line" lang="cython"> <span class="n" style="color: #333;">uint32_t</span> <span class="n" style="color: #333;">vptr_off</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">vptr_free</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># vptr offset, i.e., the size of the INFO key plus size+type bytes</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># indicates that vptr-vptr_off must be freed; set only when modified and the new</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cython"></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">@@ -164,12 +163,12 @@ cdef extern from "htslib/vcf.h":</td>
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">indiv_dirty</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># if set, indiv.s must be recreated on BCF output</span></span>
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="cython"> <span class="k" style="font-weight: 600;">ctypedef</span> <span class="kr" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">bcf1_t</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// POS</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cython"> <span class="n" style="color: #333;">int64_t</span> <span class="n" style="color: #333;">rlen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// length of REF</span></span>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cython"> <span class="n" style="color: #333;">int32_t</span> <span class="n" style="color: #333;">rid</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// CHROM</span></span>
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cython"> <span class="n" style="color: #333;">int32_t</span> <span class="n" style="color: #333;">pos</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// POS</span></span>
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169
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<pre style="margin: 0;">-<span id="LC169" class="line" lang="cython"> <span class="n" style="color: #333;">int32_t</span> <span class="n" style="color: #333;">rlen</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// length of REF</span></span>
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170
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">float</span> <span class="n" style="color: #333;">qual</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// QUAL</span></span>
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171
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cython"> <span class="n" style="color: #333;">uint32_t</span> <span class="n" style="color: #333;">n_info</span><span class="p">,</span> <span class="n" style="color: #333;">n_allele</span><span class="p">;</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">8</span>_t</span> <span class="n" style="color: #333;">n_fmt</span> <span class="c1" style="color: #998; font-style: italic;">#//:8 #//, n_sample:24;</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">uint<span class="idiff left right">32</span>_t</span> <span class="n" style="color: #333;">n_fmt</span> <span class="c1" style="color: #998; font-style: italic;">#//:8 #//, n_sample:24;</span></span>
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173
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">#kstring_t shared, indiv;</span></span>
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174
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173
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="cython"> <span class="n" style="color: #333;">bcf_dec_t</span> <span class="n" style="color: #333;">d</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#// lazy evaluation: $d is not generated by bcf_read(), but by explicitly calling bcf_unpack()</span></span>
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175
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">max_unpack</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># // Set to BCF_UN_STR, BCF_UN_FLT, or BCF_UN_INFO to boost performance of vcf_parse when some of the fields wont be needed</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="215" 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="214" 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">@@ -215,6 +214,7 @@ cdef extern from "htslib/vcf.h":</td>
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<pre style="margin: 0;"> <span id="LC214" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="n" style="color: #333;">nsamples_ori</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;"># for bcf_hdr_set_samples()</span></span>
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216
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<pre style="margin: 0;"> <span id="LC215" class="line" lang="cython"> <span class="n" style="color: #333;">uint8_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keep_samples</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">kstring_t</span> <span class="n" style="color: #333;">mem</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">m</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cython"></span>
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219
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cython"> <span class="n" style="color: #333;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_float_set</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ptr</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">value</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="235" 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">@@ -235,6 +235,8 @@ cdef extern from "htslib/vcf.h":</td>
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_nsamples</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</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 class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cython"> <span class="n" style="color: #333;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_destroy</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</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 class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cython"> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_fmt_text</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</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 class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_bcf</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">len</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_format</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</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 class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">is_bcf</span><span class="p">,</span> <span class="n" style="color: #333;">kstring_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nb" style="color: #0086b3;">str</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cython"> <span class="n" style="color: #333;">bcf_hdr_t</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_init</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mode</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_parse</span><span class="p">(</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 class="p">,</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">htxt</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cython"></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">@@ -280,7 +282,7 @@ cdef extern from "htslib/vcf.h":</td>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cython"></span>
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">## genotypes</span></span>
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cython"> <span class="n" style="color: #333;"><span class="idiff left">inline</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_gt2alleles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">igt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cython"> <span class="n" style="color: #333;">void</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_gt2alleles</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">igt</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">a</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_update_genotypes</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">const</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 class="p">,</span> <span class="n" style="color: #333;">bcf1_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">line</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">const</span> <span class="n" style="color: #333;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># idx is 0 for ref, 1... for alts...</span></span>
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">int</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_gt_phased</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">idx</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#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">@@ -11,7 +11,10 @@ import numpy as np</td>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">array</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">array</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="cython"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">math</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cython"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">ctypes</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="cython"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cython"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cython"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cython"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cython"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span> <span class="c1" style="color: #998; font-style: italic;"># python 2 backport</span></span>
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15
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cython"></span>
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16
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cython"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">libc</span> <span class="kn" style="font-weight: 600;">cimport</span> <span class="n" style="color: #333;">stdlib</span></span>
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17
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cython"><span class="kn" style="font-weight: 600;">cimport</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,7 +133,87 @@ cdef set_constants(VCF v):</td>
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130
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133
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="cython"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">HOM_ALT</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span></span>
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131
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134
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="cython"></span>
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132
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135
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="cython"></span>
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133
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VCF</span><span class="p">:</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cython"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">HTSFile</span><span class="p">:</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cython"></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hts</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">fname</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">mode</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">from_path</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cython"></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="nf" style="color: #900; font-weight: 600;">_open_htsfile</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="LC145" class="line" lang="cython"> <span class="s" style="color: #d14;">"""Opens an htsfile for reading or writing.</span></span>
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146
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cython"><span class="s" style="color: #d14;"> Parameters</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cython"><span class="s" style="color: #d14;"> ----------</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cython"><span class="s" style="color: #d14;"> fname: str</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cython"><span class="s" style="color: #d14;"> filename (str or Path), file descriptor (int), or file-like object (has fileno method).</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cython"><span class="s" style="color: #d14;"> mode: str</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cython"><span class="s" style="color: #d14;"> the mode to pass to hts_open.</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">hFILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hf</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cython"> <span class="n" style="color: #333;">reading</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">b"r"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span></span>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">reading</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">b"w"</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"No 'r' or 'w' in mode %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># for htslib, wbu seems to not work</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b"wbu"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="s" style="color: #d14;">b"wb0"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">basestring</span><span class="p">,</span> <span class="n" style="color: #333;">Path</span><span class="p">)):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">))</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b"-"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="s" style="color: #d14;">b"/dev/stdin"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reading</span> <span class="k" style="font-weight: 600;">else</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="s" style="color: #d14;">b"/dev/stdout"</span><span class="p">)</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">b".gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b"w"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">b"wz"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">((</span><span class="s" style="color: #d14;">b".bcf"</span><span class="p">,</span> <span class="s" style="color: #d14;">b".bcf.gz"</span><span class="p">))</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b"w"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">b"wb"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># from a file descriptor</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cython"> <span class="n" style="color: #333;">hf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hdopen</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_hopen</span><span class="p">(</span><span class="n" style="color: #333;">hf</span><span class="p">,</span> <span class="s" style="color: #d14;">"<file>"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="181" 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">
181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># reading from a File object or other object with fileno</span></span>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">hasattr</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="s" style="color: #d14;">"fileno"</span><span class="p">):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">closed</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">'I/O operation on closed file'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cython"> <span class="n" style="color: #333;">hf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hdopen</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">fileno</span><span class="p">(),</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_hopen</span><span class="p">(</span><span class="n" style="color: #333;">hf</span><span class="p">,</span> <span class="s" style="color: #d14;">"<file>"</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># .name can be TextIOWrapper</span></span>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cython"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cython"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">AttributeError</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<td class="diff-line-num new new_line" data-linenumber="193" 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">
193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="194" 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">
194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot open '%s' for writing."</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="195" 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">
195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cython"></span>
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</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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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error opening %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reading</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vcf</span> <span class="ow" style="font-weight: 600;">and</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bcf</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="200" 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">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cython"> <span class="s" style="color: #d14;">"%s is not valid bcf or vcf (format: %s mode: %s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fname</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cython"> <span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="204" 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">
204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">text_format</span> <span class="ow" style="font-weight: 600;">and</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">binary_format</span><span class="p">:</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="205" 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">
205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span></span>
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<td class="diff-line-num new old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cython"> <span class="s" style="color: #d14;">"%s is not valid text_format or binary_format (format: %s mode: %s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">fname</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
</pre>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cython"> <span class="p">)</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cython"></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</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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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">from_path</span><span class="p">:</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">hts_close</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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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cython"></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cython"></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">HTSFile</span><span class="p">):</span></span>
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134
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217
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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135
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218
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cython"><span class="s" style="color: #d14;"> VCF class holds methods to iterate over and query a VCF.</span></span>
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136
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219
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<pre style="margin: 0;"> <span id="LC219" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" 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="229" 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">@@ -146,6 +229,8 @@ cdef class VCF:</td>
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146
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229
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="cython"><span class="s" style="color: #d14;"> if True, then any '.' present in a genotype will classify the corresponding element in the gt_types array as UNKNOWN.</span></span>
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147
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230
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cython"><span class="s" style="color: #d14;"> samples: list</span></span>
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148
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231
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cython"><span class="s" style="color: #d14;"> list of samples to extract from full set in file.</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cython"><span class="s" style="color: #d14;"> threads: int</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cython"><span class="s" style="color: #d14;"> the number of threads to use including this reader.</span></span>
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149
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234
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="cython"></span>
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150
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235
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cython"></span>
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151
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236
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cython"><span class="s" style="color: #d14;"> Returns</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" 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="238" 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">@@ -153,13 +238,11 @@ cdef class VCF:</td>
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153
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cython"><span class="s" style="color: #d14;"> VCF object for iterating and querying.</span></span>
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154
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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155
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cython"></span>
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156
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<pre style="margin: 0;">-<span id="LC156" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">htsFile</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hts</span></span>
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<td class="diff-line-num old_line" data-linenumber="157" 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">
157
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<td class="diff-line-num new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">const</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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<td class="diff-line-num old_line" data-linenumber="158" 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">
158
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<td class="diff-line-num new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">tbx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">idx</span></span>
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159
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<td class="diff-line-num new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">hts_idx_t</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hidx</span></span>
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160
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<td class="diff-line-num new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_samples</span></span>
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161
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<td class="diff-line-num new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">PASS</span></span>
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162
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<pre style="margin: 0;">-<span id="LC162" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bytes</span> <span class="n" style="color: #333;">fname</span></span>
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163
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">gts012</span></span>
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164
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<td class="diff-line-num new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">lazy</span></span>
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165
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248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">bint</span> <span class="n" style="color: #333;">strict_gt</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" 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="261" 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">@@ -178,25 +261,8 @@ cdef class VCF:</td>
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178
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">readonly</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">UNKNOWN</span></span>
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179
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cython"></span>
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180
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<td class="diff-line-num new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"r"</span><span class="p">,</span> <span class="n" style="color: #333;">gts012</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">lazy</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">strict_gt</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">hFILE</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hf</span></span>
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<td class="diff-line-num old old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="cython"></span>
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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
183
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">basestring</span><span class="p">):</span></span>
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<td class="diff-line-num old old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
184
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<pre style="margin: 0;">-<span id="LC184" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">b"-"</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
185
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<pre style="margin: 0;">-<span id="LC185" class="line" lang="cython"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">b"/dev/stdin"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
186
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<pre style="margin: 0;">-<span id="LC186" class="line" lang="cython"> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">),</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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187
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<pre style="margin: 0;">-<span id="LC187" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_open</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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188
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<pre style="margin: 0;">-<span id="LC188" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname</span></span>
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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
189
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<td class="diff-line-num new_line old" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC189" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">-<span id="LC191" class="line" lang="cython"> <span class="n" style="color: #333;">hf</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hdopen</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</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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192
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_hopen</span><span class="p">(</span><span class="n" style="color: #333;">hf</span><span class="p">,</span> <span class="s" style="color: #d14;">"<file>"</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="p">)</span></span>
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193
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<pre style="margin: 0;">-<span id="LC193" class="line" lang="cython"></span>
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194
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<pre style="margin: 0;">-<span id="LC194" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</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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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
195
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<pre style="margin: 0;">-<span id="LC195" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"Error opening %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
196
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<td class="diff-line-num new_line old" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC196" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">vcf</span> <span class="ow" style="font-weight: 600;">and</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 class="nb" style="color: #0086b3;">format</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">bcf</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
197
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<td class="diff-line-num new_line old" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC197" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">IOError</span><span class="p">(</span><span class="s" style="color: #d14;">"%s if not valid bcf or vcf"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
198
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<pre style="margin: 0;">-<span id="LC198" class="line" lang="cython"></span>
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199
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264
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<pre style="margin: 0;"> <span id="LC264" 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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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" 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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200
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266
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<pre style="margin: 0;"> <span id="LC266" 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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<td class="diff-line-num old_line" data-linenumber="201" 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">
201
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<td class="diff-line-num new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;"> <span id="LC267" 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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202
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268
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<pre style="margin: 0;"> <span id="LC268" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="367" 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="433" 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">@@ -367,7 +433,7 @@ cdef class VCF:</td>
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367
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<td class="diff-line-num new_line" data-linenumber="433" 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">
433
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span></span>
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<td class="diff-line-num old_line" data-linenumber="368" 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">
368
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<td class="diff-line-num new_line" data-linenumber="434" 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">
434
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<pre style="margin: 0;"> <span id="LC434" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">StopIteration</span></span>
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369
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<td class="diff-line-num new_line" data-linenumber="435" 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">
435
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<pre style="margin: 0;"> <span id="LC435" class="line" lang="cython"></span>
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370
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<pre style="margin: 0;">-<span id="LC370" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="n" style="color: #333;">ENC</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'.bcf'</span></span><span class="p">):</span></span>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="n" style="color: #333;">ENC</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(<span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'.bcf'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'.bcf.gz'</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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371
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<pre style="margin: 0;"> <span id="LC437" class="line" lang="cython"> <span class="k" style="font-weight: 600;">yield</span> <span class="k" style="font-weight: 600;">from</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_bcf_region</span><span class="p">(</span><span class="n" style="color: #333;">region</span><span class="p">)</span></span>
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372
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438
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<pre style="margin: 0;"> <span id="LC438" class="line" lang="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">StopIteration</span></span>
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373
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439
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<pre style="margin: 0;"> <span id="LC439" class="line" lang="cython"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="491" 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="557" 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">@@ -491,13 +557,6 @@ cdef class VCF:</td>
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491
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557
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<pre style="margin: 0;"> <span id="LC557" class="line" lang="cython"></span>
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492
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558
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<pre style="margin: 0;"> <span id="LC558" class="line" lang="cython"> <span class="n" style="color: #333;">contains</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">__contains__</span></span>
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493
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559
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<pre style="margin: 0;"> <span id="LC559" class="line" lang="cython"></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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495
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</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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496
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>
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497
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># TODO flush</span></span>
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498
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">hts_close</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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499
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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500
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<pre style="margin: 0;">-<span id="LC500" class="line" lang="cython"></span>
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501
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<pre style="margin: 0;"> <span id="LC560" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__dealloc__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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502
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561
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<pre style="margin: 0;"> <span id="LC561" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">NULL</span> <span class="ow" style="font-weight: 600;">and</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="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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503
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562
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<pre style="margin: 0;"> <span id="LC562" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_destroy</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="533" 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="592" 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">@@ -533,11 +592,12 @@ cdef class VCF:</td>
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533
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592
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">str</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 class="n" style="color: #333;">samples</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="s" style="color: #d14;">'utf-8'</span><span class="p">))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">)]</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">raw_header</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC536" class="line" lang="cython"> <span class="s" style="color: #d14;">"string of the raw header from the VCF"</span></span>
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<pre style="margin: 0;">-<span id="LC537" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__get__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC538" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">hlen</span></span>
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<pre style="margin: 0;">-<span id="LC539" class="line" lang="cython"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_fmt_text</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 class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hlen</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC540" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">from_bytes</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cython"> <span class="s" style="color: #d14;">"string of the raw header from the VCF"</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__get__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">kstring_t</span> <span class="n" style="color: #333;">s</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cython"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">l</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">m</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_format</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 class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">from_bytes</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">s</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">seqlens</span><span class="p">:</span></span>
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__get__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="558" 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">@@ -558,7 +618,7 @@ cdef class VCF:</td>
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558
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618
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<pre style="margin: 0;"> <span id="LC618" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">cnames</span></span>
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559
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619
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<pre style="margin: 0;"> <span id="LC619" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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560
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620
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<pre style="margin: 0;"> <span id="LC620" class="line" lang="cython"> <span class="n" style="color: #333;">cnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_seqnames</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 class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n</span><span class="p">)</span></span>
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561
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<pre style="margin: 0;">-<span id="LC561" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="n" style="color: #333;">ENC</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">'.bcf'</span></span><span class="p">):</span></span>
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<td class="diff-line-num new new_line" data-linenumber="621" 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">
621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">and</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">(</span><span class="n" style="color: #333;">ENC</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(<span class="idiff left">(</span></span><span class="s" style="color: #d14;"><span class="idiff">'.bcf'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'.bcf.gz'</span></span><span class="p"><span class="idiff right">)</span>):</span></span>
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<td class="diff-line-num old_line" data-linenumber="562" 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">
562
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<td class="diff-line-num new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hidx</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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<td class="diff-line-num old_line" data-linenumber="563" 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">
563
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<td class="diff-line-num new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hidx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_index_load</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="564" 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">
564
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<td class="diff-line-num new_line" data-linenumber="624" 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">
624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hidx</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1091" 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="1151" 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">@@ -1091,7 +1151,7 @@ cdef class Variant(object):</td>
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<td class="diff-line-num old_line" data-linenumber="1091" 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">
1091
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<td class="diff-line-num new_line" data-linenumber="1151" 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">
1151
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<pre style="margin: 0;"> <span id="LC1151" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">list</span> <span class="n" style="color: #333;">d</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">from_bytes</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">alleles</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">n_allele</span><span class="p">)]</span></span>
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<td class="diff-line-num old_line" data-linenumber="1092" 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">
1092
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<td class="diff-line-num new_line" data-linenumber="1152" 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">
1152
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<pre style="margin: 0;"> <span id="LC1152" class="line" lang="cython"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">append</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;"># -1 gives .</span></span>
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<td class="diff-line-num old_line" data-linenumber="1093" 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">
1093
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<td class="diff-line-num new_line" data-linenumber="1153" 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">
1153
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<pre style="margin: 0;"> <span id="LC1153" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">list</span> <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"./."</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">)]</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1094" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1094
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<td class="diff-line-num new_line old" data-linenumber="1154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1094" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</span> <span class="n" style="color: #333;">phased</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">gt_phases</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1095" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1154" 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">
1154
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<pre style="margin: 0;">+<span id="LC1154" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">ndarray</span> <span class="n" style="color: #333;">phased</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_phases</span></span><span class="p"><span class="idiff">).</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">astype</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1095" 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">
1095
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<td class="diff-line-num new_line" data-linenumber="1155" 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">
1155
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<pre style="margin: 0;"> <span id="LC1155" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">list</span> <span class="n" style="color: #333;">lookup</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"/"</span><span class="p">,</span> <span class="s" style="color: #d14;">"|"</span><span class="p">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="1096" 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">
1096
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<td class="diff-line-num new_line" data-linenumber="1156" 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">
1156
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<pre style="margin: 0;"> <span id="LC1156" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unknown</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">gts012</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">2</span></span>
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<td class="diff-line-num old_line" data-linenumber="1097" 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">
1097
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<td class="diff-line-num new_line" data-linenumber="1157" 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">
1157
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<pre style="margin: 0;"> <span id="LC1157" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">n</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;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1142" 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="1202" 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">@@ -1142,7 +1202,7 @@ cdef class Variant(object):</td>
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<td class="diff-line-num old_line" data-linenumber="1142" 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">
1142
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<td class="diff-line-num new_line" data-linenumber="1202" 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">
1202
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<pre style="margin: 0;"> <span id="LC1202" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n</span></span>
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<td class="diff-line-num old_line" data-linenumber="1143" 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">
1143
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<td class="diff-line-num new_line" data-linenumber="1203" 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">
1203
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<pre style="margin: 0;"> <span id="LC1203" class="line" lang="cython"></span>
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1144
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<td class="diff-line-num new_line" data-linenumber="1204" 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">
1204
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<pre style="margin: 0;"> <span id="LC1204" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">call_rate</span><span class="p">:</span></span>
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1145
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<td class="diff-line-num new_line old" data-linenumber="1205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1145" class="line" lang="cython"> <span class="s" style="color: #d14;">"proprtion of samples that were not UNKNOWN."</span></span>
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1205
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<pre style="margin: 0;">+<span id="LC1205" class="line" lang="cython"> <span class="s" style="color: #d14;">"prop<span class="idiff left right">o</span>rtion of samples that were not UNKNOWN."</span></span>
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1146
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<td class="diff-line-num new_line" data-linenumber="1206" 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">
1206
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<pre style="margin: 0;"> <span id="LC1206" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__get__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1147
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<td class="diff-line-num new_line" data-linenumber="1207" 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">
1207
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<pre style="margin: 0;"> <span id="LC1207" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1148
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<td class="diff-line-num new_line" data-linenumber="1208" 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">
1208
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<pre style="margin: 0;"> <span id="LC1208" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">num_called</span><span class="p">)</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;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1287" 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="1347" 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">@@ -1287,7 +1347,7 @@ cdef class Variant(object):</td>
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1287
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<td class="diff-line-num new_line" data-linenumber="1347" 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">
1347
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<pre style="margin: 0;"> <span id="LC1347" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ndst</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="diff-line-num old_line" data-linenumber="1288" 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">
1288
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<td class="diff-line-num new_line" data-linenumber="1348" 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">
1348
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<pre style="margin: 0;"> <span id="LC1348" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_get_genotypes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">gts</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ndst</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1289
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<td class="diff-line-num new_line" data-linenumber="1349" 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">
1349
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<pre style="margin: 0;"> <span id="LC1349" 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;">"couldn't get genotypes for variant"</span><span class="p">)</span></span>
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1290
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<pre style="margin: 0;">-<span id="LC1290" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">newGenotypes</span><span class="p">(</span><span class="n" style="color: #333;">gts</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">ndst</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1350" 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">
1350
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<pre style="margin: 0;">+<span id="LC1350" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">newGenotypes</span><span class="p">(</span><span class="n" style="color: #333;">gts</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ndst</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">)</span></span>
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1291
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cython"></span>
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1292
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="n" style="color: #333;">genotype</span><span class="p">.</span><span class="n" style="color: #333;">setter</span></span>
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1293
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<td class="diff-line-num new_line" data-linenumber="1353" 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">
1353
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<pre style="margin: 0;"> <span id="LC1353" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">genotype</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">Genotypes</span> <span class="n" style="color: #333;">g</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1380" 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="1440" 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">@@ -1380,10 +1440,10 @@ cdef class Variant(object):</td>
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1380
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1440
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<pre style="margin: 0;"> <span id="LC1440" class="line" lang="cython"> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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1381
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1441
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<pre style="margin: 0;"> <span id="LC1441" class="line" lang="cython"></span>
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1382
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<td class="diff-line-num new_line" data-linenumber="1442" 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">
1442
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<pre style="margin: 0;"> <span id="LC1442" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">ret</span></span>
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1383
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<td class="diff-line-num new_line old" data-linenumber="1443" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1383" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">issubdtype</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">int</span></span><span class="p">):</span></span>
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1443
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<pre style="margin: 0;">+<span id="LC1443" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">issubdtype</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">signedinteger</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="nf" style="color: #900; font-weight: 600;"><span class="idiff">issubdtype</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">data</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">dtype</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">np</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">unsignedinteger</span></span><span class="p">):</span></span>
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1384
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<td class="diff-line-num new_line" data-linenumber="1444" 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">
1444
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<pre style="margin: 0;"> <span id="LC1444" class="line" lang="cython"> <span class="n" style="color: #333;">aint</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">reshape</span><span class="p">((</span><span class="n" style="color: #333;">size</span><span class="p">,))</span></span>
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<td class="diff-line-num old_line" data-linenumber="1385" 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">
1385
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<td class="diff-line-num new_line" data-linenumber="1445" 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">
1445
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<pre style="margin: 0;"> <span id="LC1445" class="line" lang="cython"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_update_format_int32</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">aint</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1386
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<td class="diff-line-num new_line old" data-linenumber="1446" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1386" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">issubdtype</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">float</span><span class="p">):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1446" 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">
1446
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<pre style="margin: 0;">+<span id="LC1446" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">issubdtype</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">dtype</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float<span class="idiff left right">ing</span></span><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="1387" 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">
1387
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<td class="diff-line-num new_line" data-linenumber="1447" 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">
1447
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<pre style="margin: 0;"> <span id="LC1447" class="line" lang="cython"> <span class="n" style="color: #333;">afloat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">astype</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float32</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">reshape</span><span class="p">((</span><span class="n" style="color: #333;">size</span><span class="p">,))</span></span>
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<td class="diff-line-num old_line" data-linenumber="1388" 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">
1388
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<td class="diff-line-num new_line" data-linenumber="1448" 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">
1448
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<pre style="margin: 0;"> <span id="LC1448" class="line" lang="cython"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_update_format_float</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">afloat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">size</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1389" 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">
1389
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<td class="diff-line-num new_line" data-linenumber="1449" 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">
1449
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<pre style="margin: 0;"> <span id="LC1449" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1404" 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="1464" 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">@@ -1404,7 +1464,7 @@ cdef class Variant(object):</td>
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1404
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<td class="diff-line-num new_line" data-linenumber="1464" 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">
1464
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<pre style="margin: 0;"> <span id="LC1464" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_types</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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<td class="diff-line-num old_line" data-linenumber="1405" 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">
1405
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<td class="diff-line-num new_line" data-linenumber="1465" 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">
1465
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<pre style="margin: 0;"> <span id="LC1465" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_phased</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*></span><span class="n" style="color: #333;">stdlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">malloc</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sizeof</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</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;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">)</span></span>
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1406
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<td class="diff-line-num new_line" data-linenumber="1466" 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">
1466
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<pre style="margin: 0;"> <span id="LC1466" class="line" lang="cython"> <span class="n" style="color: #333;">ngts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_get_genotypes</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</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;">_gt_types</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ndst</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1407
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<td class="diff-line-num new_line old" data-linenumber="1467" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1407" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ndst</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span></span>
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1467
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<pre style="margin: 0;">+<span id="LC1467" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">ndst</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1408
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<td class="diff-line-num new_line" data-linenumber="1468" 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">
1468
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<pre style="margin: 0;"> <span id="LC1468" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_ploidy</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nper</span></span>
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<td class="diff-line-num old_line" data-linenumber="1409" 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">
1409
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<td class="diff-line-num new_line" data-linenumber="1469" 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">
1469
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<pre style="margin: 0;"> <span id="LC1469" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_idxs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">int</span> <span class="o" style="font-weight: 600;">*></span><span class="n" style="color: #333;">stdlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">malloc</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sizeof</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</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;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nper</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1410" 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">
1410
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<td class="diff-line-num new_line" data-linenumber="1470" 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">
1470
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<pre style="margin: 0;"> <span id="LC1470" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ndst</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1460" 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="1520" 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">@@ -1460,7 +1520,7 @@ cdef class Variant(object):</td>
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1460
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<td class="diff-line-num new_line" data-linenumber="1520" 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">
1520
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<pre style="margin: 0;"> <span id="LC1520" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_pls</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1461" 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">
1461
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<td class="diff-line-num new_line" data-linenumber="1521" 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">
1521
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<pre style="margin: 0;"> <span id="LC1521" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_pls</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">imax</span></span>
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<td class="diff-line-num old_line" data-linenumber="1462" 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">
1462
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<td class="diff-line-num new_line" data-linenumber="1522" 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">
1522
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<pre style="margin: 0;"> <span id="LC1522" class="line" lang="cython"></span>
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<td class="diff-line-num old old_line" data-linenumber="1463" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1463
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<td class="diff-line-num new_line old" data-linenumber="1523" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1463" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1464" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1523" 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">
1523
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<pre style="margin: 0;">+<span id="LC1523" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1464" 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">
1464
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<td class="diff-line-num new_line" data-linenumber="1524" 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">
1524
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<pre style="margin: 0;"> <span id="LC1524" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">npy_intp</span> <span class="n" style="color: #333;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="diff-line-num old_line" data-linenumber="1465" 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">
1465
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<td class="diff-line-num new_line" data-linenumber="1525" 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">
1525
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<pre style="margin: 0;"> <span id="LC1525" class="line" lang="cython"> <span class="kt" style="color: #458; font-weight: 600;">shape</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">npy_intp</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;">_gt_nper</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;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span></span>
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<td class="diff-line-num old_line" data-linenumber="1466" 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">
1466
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<td class="diff-line-num new_line" data-linenumber="1526" 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">
1526
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<pre style="margin: 0;"> <span id="LC1526" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_pls</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1534" 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="1594" 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">@@ -1534,7 +1594,7 @@ cdef class Variant(object):</td>
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<td class="diff-line-num old_line" data-linenumber="1534" 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">
1534
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<td class="diff-line-num new_line" data-linenumber="1594" 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">
1594
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<pre style="margin: 0;"> <span id="LC1594" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># GATK</span></span>
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<td class="diff-line-num old_line" data-linenumber="1535" 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">
1535
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<td class="diff-line-num new_line" data-linenumber="1595" 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">
1595
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<pre style="margin: 0;"> <span id="LC1595" class="line" lang="cython"> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_get_format_int32</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="s" style="color: #d14;">"AD"</span><span class="p">,</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;">_gt_ref_depths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ndst</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1536" 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">
1536
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<td class="diff-line-num new_line" data-linenumber="1596" 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">
1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1537" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1537
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<td class="diff-line-num new_line old" data-linenumber="1597" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1537" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1538" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1597" 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">
1597
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<pre style="margin: 0;">+<span id="LC1597" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<td class="diff-line-num old_line" data-linenumber="1538" 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">
1538
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<td class="diff-line-num new_line" data-linenumber="1598" 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">
1598
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<pre style="margin: 0;"> <span id="LC1598" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1539" 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">
1539
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1599
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<pre style="margin: 0;"> <span id="LC1599" class="line" lang="cython"> <span class="n" style="color: #333;">stdlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_ref_depths</span><span class="p">);</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_ref_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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1540
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<td class="diff-line-num new_line" data-linenumber="1600" 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">
1600
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<pre style="margin: 0;"> <span id="LC1600" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1575" 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="1635" 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">@@ -1575,7 +1635,7 @@ cdef class Variant(object):</td>
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1575
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<td class="diff-line-num new_line" data-linenumber="1635" 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">
1635
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<pre style="margin: 0;"> <span id="LC1635" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># GATK</span></span>
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<td class="diff-line-num old_line" data-linenumber="1576" 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">
1576
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<td class="diff-line-num new_line" data-linenumber="1636" 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">
1636
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<pre style="margin: 0;"> <span id="LC1636" class="line" lang="cython"> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_get_format_int32</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="s" style="color: #d14;">"AD"</span><span class="p">,</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;">_gt_alt_depths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ndst</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="1577" 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">
1577
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<td class="diff-line-num new_line" data-linenumber="1637" 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">
1637
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<pre style="margin: 0;"> <span id="LC1637" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1578
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<td class="diff-line-num new_line old" data-linenumber="1638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1578" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="1638" 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">
1638
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<pre style="margin: 0;">+<span id="LC1638" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1579
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<td class="diff-line-num new_line" data-linenumber="1639" 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">
1639
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<pre style="margin: 0;"> <span id="LC1639" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="1580" 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">
1580
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<td class="diff-line-num new_line" data-linenumber="1640" 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">
1640
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<pre style="margin: 0;"> <span id="LC1640" class="line" lang="cython"> <span class="n" style="color: #333;">stdlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_alt_depths</span><span class="p">);</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_alt_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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<td class="diff-line-num old_line" data-linenumber="1581" 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">
1581
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<td class="diff-line-num new_line" data-linenumber="1641" 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">
1641
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<pre style="margin: 0;"> <span id="LC1641" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1590" 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="1650" 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">@@ -1590,7 +1650,7 @@ cdef class Variant(object):</td>
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1590
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1650
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<pre style="margin: 0;"> <span id="LC1650" class="line" lang="cython"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1591
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<td class="diff-line-num new_line" data-linenumber="1651" 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">
1651
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<pre style="margin: 0;"> <span id="LC1651" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># Freebayes</span></span>
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<td class="diff-line-num old_line" data-linenumber="1592" 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">
1592
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<td class="diff-line-num new_line" data-linenumber="1652" 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">
1652
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<pre style="margin: 0;"> <span id="LC1652" class="line" lang="cython"> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_get_format_int32</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">b</span><span class="p">,</span> <span class="s" style="color: #d14;">"AO"</span><span class="p">,</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;">_gt_alt_depths</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ndst</span><span class="p">)</span></span>
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1593
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<td class="diff-line-num new_line old" data-linenumber="1653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC1593" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">n_samples</span></span></span>
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1653
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<pre style="margin: 0;">+<span id="LC1653" class="line" lang="cython"> <span class="n" style="color: #333;">nper</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">nret</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="bp" style="color: #999;"><span class="idiff">self</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vcf</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">n_samples</span></span><span class="p"><span class="idiff right">)</span></span></span>
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1594
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1654
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<pre style="margin: 0;"> <span id="LC1654" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nret</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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1595
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1655
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<pre style="margin: 0;"> <span id="LC1655" class="line" lang="cython"> <span class="n" style="color: #333;">stdlib</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">free</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_alt_depths</span><span class="p">);</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_alt_depths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NULL</span></span>
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1596
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<td class="diff-line-num new_line" data-linenumber="1656" 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">
1656
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<pre style="margin: 0;"> <span id="LC1656" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">zeros</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1684" 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="1744" 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">@@ -1684,7 +1744,7 @@ cdef class Variant(object):</td>
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1684
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1744
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<pre style="margin: 0;"> <span id="LC1744" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">depth</span></span>
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1685
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1745
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<pre style="margin: 0;"> <span id="LC1745" class="line" lang="cython"></span>
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1686
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1746
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<pre style="margin: 0;"> <span id="LC1746" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">gt_phases</span><span class="p">:</span></span>
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1687
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<pre style="margin: 0;">-<span id="LC1687" class="line" lang="cython"> <span class="s" style="color: #d14;">"""get a boolean indicating wether each sample is phased as a numpy array."""</span></span>
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1747
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<pre style="margin: 0;">+<span id="LC1747" class="line" lang="cython"> <span class="s" style="color: #d14;">"""get a boolean indicating w<span class="idiff left right">h</span>ether each sample is phased as a numpy array."""</span></span>
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1688
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1748
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<pre style="margin: 0;"> <span id="LC1748" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__get__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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1689
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1749
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<pre style="margin: 0;"> <span id="LC1749" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># run for side-effect</span></span>
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1690
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1750
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<pre style="margin: 0;"> <span id="LC1750" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_phased</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2154" 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="2214" 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">@@ -2154,6 +2214,7 @@ cdef from_bytes(s):</td>
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2154
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2214
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<pre style="margin: 0;"> <span id="LC2214" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">s</span></span>
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2155
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2215
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<pre style="margin: 0;"> <span id="LC2215" class="line" lang="cython"></span>
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2156
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2216
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<pre style="margin: 0;"> <span id="LC2216" class="line" lang="cython"></span>
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2217
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<pre style="margin: 0;">+<span id="LC2217" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;"># TODO: make Writer extend HTSFile not VCF by moving common methods into HTSFile</span></span>
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2157
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2218
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<pre style="margin: 0;"> <span id="LC2218" class="line" lang="cython"><span class="k" style="font-weight: 600;">cdef</span> <span class="kr" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">VCF</span><span class="p">):</span></span>
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2158
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2219
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<pre style="margin: 0;"> <span id="LC2219" class="line" lang="cython"> <span class="s" style="color: #d14;">"""</span></span>
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2159
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2220
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<pre style="margin: 0;"> <span id="LC2220" class="line" lang="cython"><span class="s" style="color: #d14;"> Writer class makes a VCF Writer.</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2237" 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">@@ -2176,15 +2237,7 @@ cdef class Writer(VCF):</td>
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2176
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2237
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<pre style="margin: 0;"> <span id="LC2237" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">const</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;">ohdr</span></span>
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2177
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2238
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<pre style="margin: 0;"> <span id="LC2238" class="line" lang="cython"></span>
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2178
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<pre style="margin: 0;"> <span id="LC2239" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">Writer</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">VCF</span> <span class="n" style="color: #333;">tmpl</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">):</span></span>
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2179
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2179" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2180
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2180" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2181" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2181
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2181" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wz"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2182
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2182" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".bcf"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2183
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2183" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2184
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2184" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2185
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2185" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</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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<td class="diff-line-num old old_line" data-linenumber="2186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2186
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2186" 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;">"error opening file: %s"</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;">name</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2187
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<td class="diff-line-num new_line old" data-linenumber="2240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2187" class="line" lang="cython"></span>
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2240
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<pre style="margin: 0;">+<span id="LC2240" 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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2188
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<td class="diff-line-num new_line" data-linenumber="2241" 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">
2241
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<pre style="margin: 0;"> <span id="LC2241" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_sync</span><span class="p">(</span><span class="n" style="color: #333;">tmpl</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="2189" 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">
2189
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<td class="diff-line-num new_line" data-linenumber="2242" 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">
2242
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<pre style="margin: 0;"> <span id="LC2242" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ohdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tmpl</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span></span>
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<td class="diff-line-num old_line" data-linenumber="2190" 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">
2190
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<td class="diff-line-num new_line" data-linenumber="2243" 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">
2243
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<pre style="margin: 0;"> <span id="LC2243" class="line" lang="cython"> <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_dup</span><span class="p">(</span><span class="n" style="color: #333;">tmpl</span><span class="p">.</span><span class="n" style="color: #333;">hdr</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2194" 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="2247" 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">@@ -2194,14 +2247,8 @@ cdef class Writer(VCF):</td>
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2194
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">classmethod</span></span>
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<td class="diff-line-num old_line" data-linenumber="2195" 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">
2195
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<td class="diff-line-num new_line" data-linenumber="2248" 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">
2248
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<pre style="margin: 0;"> <span id="LC2248" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">from_string</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">Writer</span> <span class="n" style="color: #333;">cls</span><span class="p">,</span> <span class="n" style="color: #333;">fname</span><span class="p">,</span> <span class="n" style="color: #333;">header_string</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"w"</span><span class="p">):</span></span>
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<td class="diff-line-num old_line" data-linenumber="2196" 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">
2196
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<td class="diff-line-num new_line" data-linenumber="2249" 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">
2249
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<pre style="margin: 0;"> <span id="LC2249" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">Writer</span> <span class="bp" style="color: #999;">self</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Writer</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">__new__</span><span class="p">(</span><span class="n" style="color: #333;">Writer</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2197
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<td class="diff-line-num new_line old" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2197" class="line" lang="cython"></span>
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<td class="diff-line-num old old_line" data-linenumber="2198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
2198
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<td class="diff-line-num new_line old" data-linenumber="2250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC2198" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">fname</span><span class="p">)</span></span>
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2199
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<pre style="margin: 0;">-<span id="LC2199" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".gz"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span><span class="p">:</span></span>
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2200
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<pre style="margin: 0;">-<span id="LC2200" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wz"</span></span>
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2201
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<pre style="margin: 0;">-<span id="LC2201" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">".bcf"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"w"</span><span class="p">:</span></span>
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2202
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<pre style="margin: 0;">-<span id="LC2202" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb"</span></span>
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2203
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<pre style="margin: 0;">-<span id="LC2203" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">hts</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">hts_open</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="p">))</span></span>
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2204
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2250
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<pre style="margin: 0;"> <span id="LC2250" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="n" style="color: #333;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hmode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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2251
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<pre style="margin: 0;">+<span id="LC2251" 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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2205
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2252
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<pre style="margin: 0;"> <span id="LC2252" class="line" lang="cython"> <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_init</span><span class="p">(</span><span class="n" style="color: #333;">hmode</span><span class="p">)</span></span>
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2206
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2253
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<pre style="margin: 0;"> <span id="LC2253" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ohdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_dup</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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2207
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2254
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<pre style="margin: 0;"> <span id="LC2254" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_parse</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 class="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">header_string</span><span class="p">))</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>
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<li id="fd11e2e4bd1b8903c21cf95e681058bd017b76b9">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#fd11e2e4bd1b8903c21cf95e681058bd017b76b9"><strong>cyvcf2/tests/test_reader.py</strong></a>
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1
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">cyvcf2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VCF</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">Writer</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left right">..</span>cyvcf2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">VCF</span><span class="p">,</span> <span class="n" style="color: #333;">Variant</span><span class="p">,</span> <span class="n" style="color: #333;">Writer</span></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os.path</span></span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">nose.tools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">assert_raises</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -7,6 +7,11 @@ import tempfile</td>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">atexit</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib2</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span> <span class="c1" style="color: #998; font-style: italic;"># python 2 backport</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">HERE</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;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">VCF_PATH</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.vcf.gz"</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,8 +25,29 @@ except NameError:</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"> <span class="nb" style="color: #0086b3;">basestring</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">bytes</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_init</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># string</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">v</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">expected_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Path</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_count</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file descriptor</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_count</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># this should not close the file descriptor originally opened</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file-like object</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_count</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;"># this should not close the file descriptor originally opened</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_type</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -237,32 +263,46 @@ def test_writer_from_string():</td>
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python"> <span class="n" style="color: #333;">w</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_writer</span><span class="p">():</span></span>
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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mktemp</span><span class="p">(</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">".vcf"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC244" class="line" lang="python"> <span class="n" style="color: #333;">atexit</span><span class="p">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">unlink</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="python"> <span class="n" style="color: #333;">o</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_writer</span><span class="p">(</span><span class="n" style="color: #333;">writer</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">):</span></span>
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248
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">[</span><span class="s" style="color: #d14;">"AC"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"3"</span></span>
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249
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"LowQual"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">o</span></span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">writer</span></span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"LowQual"</span><span class="p">,</span> <span class="s" style="color: #d14;">"VQSRTrancheSNP99.90to100.00"</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">o</span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python"></span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="python"> <span class="n" style="color: #333;">writer</span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python"></span>
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="python"> <span class="n" style="color: #333;">rec</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</span></span>
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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">o</span></span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">writer</span></span><span class="p">.</span><span class="n" style="color: #333;">write_record</span><span class="p">(</span><span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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258
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276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"></span>
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259
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">o</span></span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left right">writer</span></span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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260
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>
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261
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"LowQual"</span><span class="p">,</span> <span class="s" style="color: #d14;">"LowQual;VQSRTrancheSNP99.90to100.00"</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">]</span></span>
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262
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python"></span>
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263
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<pre style="margin: 0;">-<span id="LC263" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">variant</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)):</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">variant</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">f<span class="idiff left right">ilename</span></span><span class="p">)):</span></span>
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264
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">],</span> <span class="p">(</span><span class="n" style="color: #333;">variant</span><span class="p">.</span><span class="n" style="color: #333;">FILTER</span><span class="p">,</span> <span class="n" style="color: #333;">expected</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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265
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python"></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_writer</span><span class="p">():</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempfile</span><span class="p">.</span><span class="n" style="color: #333;">mktemp</span><span class="p">(</span><span class="n" style="color: #333;">suffix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">".vcf"</span><span class="p">)</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"> <span class="n" style="color: #333;">atexit</span><span class="p">.</span><span class="n" style="color: #333;">register</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">unlink</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="n" style="color: #333;">rec</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># string</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">run_writer</span><span class="p">(</span><span class="n" style="color: #333;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="python"></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Path</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="python"> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"> <span class="n" style="color: #333;">run_writer</span><span class="p">(</span><span class="n" style="color: #333;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="python"></span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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="LC297" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file descriptor</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="python"> <span class="n" style="color: #333;">fd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fp</span><span class="p">.</span><span class="n" style="color: #333;">fileno</span><span class="p">()</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="python"> <span class="n" style="color: #333;">run_writer</span><span class="p">(</span><span class="n" style="color: #333;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">fd</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># file-like object</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fp</span><span class="p">:</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"> <span class="n" style="color: #333;">run_writer</span><span class="p">(</span><span class="n" style="color: #333;">Writer</span><span class="p">(</span><span class="n" style="color: #333;">fp</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">),</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">rec</span><span class="p">)</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="python"></span>
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266
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306
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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_add_info_to_header</span><span class="p">():</span></span>
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267
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307
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">VCF_PATH</span><span class="p">)</span></span>
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268
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308
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">add_info_to_header</span><span class="p">({</span><span class="s" style="color: #d14;">'ID'</span><span class="p">:</span> <span class="s" style="color: #d14;">'abcdefg'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Description'</span><span class="p">:</span> <span class="s" style="color: #d14;">'abcdefg'</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="583" 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="623" 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">@@ -583,7 +623,7 @@ def test_set_format_float():</td>
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583
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623
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python"> <span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="s" style="color: #d14;">'{}/test-format-string.vcf'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">HERE</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="584" 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">
584
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">add_format_to_header</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">ID</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PS"</span><span class="p">,</span> <span class="n" style="color: #333;">Number</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">Type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Float"</span><span class="p">,</span> <span class="n" style="color: #333;">Description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"PS example"</span><span class="p">))</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span></span>
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585
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python"> <span class="n" style="color: #333;">v</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">vcf</span><span class="p">)</span></span>
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586
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<td class="diff-line-num new_line old" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC586" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">set_format</span><span class="p">(</span><span class="s" style="color: #d14;">"PS"</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">0.555</span><span class="p">,</span> <span class="mf" style="color: #099;">1.111</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">float</span><span class="p">))</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">set_format</span><span class="p">(</span><span class="s" style="color: #d14;">"PS"</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">0.555</span><span class="p">,</span> <span class="mf" style="color: #099;">1.111</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float<span class="idiff left right">32</span></span><span class="p">))</span></span>
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587
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627
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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">fmap</span><span class="p">(</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span> <span class="n" style="color: #333;">get_gt_str</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">,</span> <span class="s" style="color: #d14;">"PS"</span><span class="p">)),</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">0.555</span><span class="p">,</span> <span class="mf" style="color: #099;">1.111</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC628" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">set_format</span><span class="p">(</span><span class="s" style="color: #d14;">"PS"</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">([</span><span class="mf" style="color: #099;">8.555</span><span class="p">,</span> <span class="mf" style="color: #099;">11.111</span><span class="p">],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float64</span><span class="p">))</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -876,18 +916,18 @@ def test_strict_gt_option_flag():</td>
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"VCF(gts012=False, strict_gt=False) not working"</span></span>
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="python"> <span class="n" style="color: #333;">truth_gt_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC879" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_bases</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_gt_bases</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} [gt_bases]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC880" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_types</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_gt_types</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} [gt_types]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC881" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genotypes</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_genotypes</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} (genotypes)'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_bases</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_gt_bases</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} [gt_bases]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_types</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_gt_types</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} [gt_types]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC921" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genotypes</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_genotypes</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} (genotypes)'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC922" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"> <span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">test_vcf</span><span class="p">,</span> <span class="n" style="color: #333;">gts012</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">strict_gt</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC924" class="line" lang="python"> <span class="n" style="color: #333;">variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">next</span><span class="p">(</span><span class="n" style="color: #333;">vcf</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC925" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC926" class="line" lang="python"> <span class="n" style="color: #333;">msg</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"VCF(gts012=False, strict_gt=True) not working"</span></span>
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<pre style="margin: 0;"> <span id="LC927" class="line" lang="python"> <span class="n" style="color: #333;">truth_gt_types</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC888" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_bases</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_gt_bases</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} [gt_bases]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC889" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_types</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_gt_types</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} [gt_types]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC890" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genotypes</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">truth_genotypes</span></span><span class="p">,</span> <span class="s" style="color: #d14;">'{} (genotypes)'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC928" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_bases</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_gt_bases</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} [gt_bases]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC929" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">gt_types</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">tolist</span></span><span class="p"><span class="idiff">())</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_gt_types</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} [gt_types]'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC930" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">bool</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">tuple</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">variant</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">genotypes</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">==</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">truth_genotypes</span></span><span class="p"><span class="idiff right">)</span>,</span> <span class="s" style="color: #d14;">'{} (genotypes)'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">msg</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC931" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC932" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC933" class="line" lang="python"> <span class="n" style="color: #333;">vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span><span class="p">(</span><span class="n" style="color: #333;">test_vcf</span><span class="p">,</span> <span class="n" style="color: #333;">gts012</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#aded7756cdea7c289134466a0d54da4f26d43abb"><strong>docs/source/conf.py</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">@@ -53,7 +53,7 @@ master_doc = 'index'</td>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'cyvcf2'</span></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2016, Brent Pedersen'</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'2016<span class="idiff left right">..2020</span>, Brent Pedersen'</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'Brent Pedersen'</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#62df078594b947ca6f787a59ae6ddefabce9fcad"><strong>docs/source/index.rst</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">@@ -60,7 +60,7 @@ Modifying Existing Records</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext">==========================</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext">`cyvcf2` is optimized for fast reading and extraction from existing files.</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="plaintext">However, it also offers some means of modifying existing VCFs. Here, w<span class="idiff left right">rapper</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">However, it also offers some means of modifying existing VCFs. Here, w<span class="idiff left right">e</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">show an example of how to annotate variants with the genes that they overlap.</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext"></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">@@ -74,7 +74,8 @@ show an example of how to annotate variants with the genes that they overlap.</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"> 'Type':'Character', 'Number': '1'})</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"> # create a new vcf Writer using the input vcf as a template.</span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext"> w = Writer(f, vcf)</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> fname = "out.vcf"</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> w = Writer(fname, vcf)</span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"> for v in vcf:</span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="plaintext"> # The get_gene_intersections function is not shown.</span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/09dacf19d9e0e0bfd2c60d38d1141c31106cffff#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span></span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">os</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">glob</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"></span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pkg_resources</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">setuptools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span><span class="p">,</span> <span class="n" style="color: #333;">dist</span></span>
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7
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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8
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">.</span><span class="n" style="color: #333;">major</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">.</span><span class="n" style="color: #333;">minor</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">7</span><span class="p">:</span></span>
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9
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"ERROR: cyvcf2 is only for python 2.7 or greater you are running %d.%d</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">.</span><span class="n" style="color: #333;">major</span><span class="p">,</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span><span class="p">.</span><span class="n" style="color: #333;">minor</span><span class="p">))</span></span>
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10
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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11
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Install numpy right now</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="n" style="color: #333;">dist</span><span class="p">.</span><span class="n" style="color: #333;">Distribution</span><span class="p">().</span><span class="n" style="color: #333;">fetch_build_eggs</span><span class="p">([</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"></span>
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_version</span><span class="p">():</span></span>
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"""Get the version info from the mpld3 package without importing it"""</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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">@@ -26,51 +32,53 @@ def get_version():</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"version could not be located"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Temporarily install dependencies required by setup.py before trying to import them.</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># From https://bitbucket.org/dholth/setup-requires</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'setup-requires'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"><span class="n" style="color: #333;">pkg_resources</span><span class="p">.</span><span class="n" style="color: #333;">working_set</span><span class="p">.</span><span class="n" style="color: #333;">add_entry</span><span class="p">(</span><span class="s" style="color: #d14;">'setup-requires'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">missing_requirements</span><span class="p">(</span><span class="n" style="color: #333;">specifiers</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">specifier</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">specifiers</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">pkg_resources</span><span class="p">.</span><span class="n" style="color: #333;">require</span><span class="p">(</span><span class="n" style="color: #333;">specifier</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="n" style="color: #333;">pkg_resources</span><span class="p">.</span><span class="n" style="color: #333;">DistributionNotFound</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"> <span class="k" style="font-weight: 600;">yield</span> <span class="n" style="color: #333;">specifier</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">install_requirements</span><span class="p">(</span><span class="n" style="color: #333;">specifiers</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"> <span class="n" style="color: #333;">to_install</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">specifiers</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">to_install</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="python"> <span class="n" style="color: #333;">cmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">executable</span><span class="p">,</span> <span class="s" style="color: #d14;">"-m"</span><span class="p">,</span> <span class="s" style="color: #d14;">"pip"</span><span class="p">,</span> <span class="s" style="color: #d14;">"install"</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="s" style="color: #d14;">"-t"</span><span class="p">,</span> <span class="s" style="color: #d14;">"setup-requires"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">to_install</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="n" style="color: #333;">cmd</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">requires</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'cython'</span><span class="p">,</span> <span class="s" style="color: #d14;">'numpy'</span><span class="p">,</span> <span class="s" style="color: #d14;">'coloredlogs'</span><span class="p">,</span> <span class="s" style="color: #d14;">'click'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="n" style="color: #333;">install_requirements</span><span class="p">(</span><span class="n" style="color: #333;">missing_requirements</span><span class="p">(</span><span class="n" style="color: #333;">requires</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">excludes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'irods'</span><span class="p">,</span> <span class="s" style="color: #d14;">'plugin'</span><span class="p">]</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python"><span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">glob</span><span class="p">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">'htslib/*.c'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">excludes</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">glob</span><span class="p">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">'htslib/cram/*.c'</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># these have main()'s</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">no_cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">_ignore</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">extension</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extensions</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">sfile</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">extension</span><span class="p">.</span><span class="n" style="color: #333;">sources</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="n" style="color: #333;">ext</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;">splitext</span><span class="p">(</span><span class="n" style="color: #333;">sfile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ext</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">".pyx"</span><span class="p">,</span> <span class="s" style="color: #d14;">".py"</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">sfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">path</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".c"</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="n" style="color: #333;">sources</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">sfile</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="n" style="color: #333;">extension</span><span class="p">.</span><span class="n" style="color: #333;">sources</span><span class="p">[:]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sources</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">extensions</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Build the Cython extension by statically linking to the bundled htslib</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">glob</span><span class="p">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">'htslib/*.c'</span><span class="p">)</span> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">any</span><span class="p">(</span><span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">[</span><span class="s" style="color: #d14;">'irods'</span><span class="p">,</span> <span class="s" style="color: #d14;">'plugin'</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="p">]</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">glob</span><span class="p">.</span><span class="n" style="color: #333;">glob</span><span class="p">(</span><span class="s" style="color: #d14;">'htslib/cram/*.c'</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Exclude the htslib sources containing main()'s</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="n" style="color: #333;">sources</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sources</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">x</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">((</span><span class="s" style="color: #d14;">'htsfile.c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'tabix.c'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bgzip.c'</span><span class="p">))]</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">sources</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="s" style="color: #d14;">'cyvcf2/helpers.c'</span><span class="p">)</span></span>
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62
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">platform</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Distutils</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">build_ext</span></span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="python"></span>
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67
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="n" style="color: #333;">cmdclass</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'build_ext'</span><span class="p">:</span> <span class="n" style="color: #333;">build_ext</span><span class="p">}</span></span>
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68
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="python"><span class="n" style="color: #333;">extension</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"cyvcf2.cyvcf2"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">Extension</span><span class="p">(</span><span class="s" style="color: #d14;">"cyvcf2.cyvcf2"</span><span class="p">,</span></span>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"> <span class="p">[</span><span class="s" style="color: #d14;">"cyvcf2/cyvcf2.pyx"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">sources</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">libraries</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'z'</span><span class="p">,</span> <span class="s" style="color: #d14;">'bz2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'lzma'</span><span class="p">,</span> <span class="s" style="color: #d14;">'curl'</span><span class="p">,</span> <span class="s" style="color: #d14;">'ssl'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">([</span><span class="s" style="color: #d14;">'crypt'</span><span class="p">]</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">platform</span><span class="p">.</span><span class="n" style="color: #333;">system</span><span class="p">()</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'Darwin'</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">[]),</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">extra_compile_args</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"-Wno-sign-compare"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Wno-unused-function"</span><span class="p">,</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="s" style="color: #d14;">"-Wno-strict-prototypes"</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="s" style="color: #d14;">"-Wno-unused-result"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-Wno-discarded-qualifiers"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="n" style="color: #333;">include_dirs</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'htslib'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cyvcf2'</span><span class="p">,</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">get_include</span><span class="p">()])]</span></span>
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72
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"></span>
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"><span class="n" style="color: #333;">CYTHONIZE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">bool</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">getenv</span><span class="p">(</span><span class="s" style="color: #d14;">"CYTHONIZE"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)))</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">CYTHONIZE</span><span class="p">:</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Cython.Build</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">cythonize</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"> <span class="s" style="color: #d14;">"Cannot find Cython. Have you installed all the requirements?</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="s" style="color: #d14;">"Try pip install -r requirements.txt</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"> <span class="p">)</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">compiler_directives</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"language_level"</span><span class="p">:</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="s" style="color: #d14;">"embedsignature"</span><span class="p">:</span> <span class="bp" style="color: #999;">True</span><span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span> <span class="n" style="color: #333;">compiler_directives</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">compiler_directives</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">no_cythonize</span><span class="p">(</span><span class="n" style="color: #333;">extensions</span><span class="p">)</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="python"></span>
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74
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82
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>
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75
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83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"cyvcf2"</span><span class="p">,</span></span>
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76
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"fast vcf parsing with cython + htslib"</span><span class="p">,</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,8 +89,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Brent Pedersen"</span><span class="p">,</span></span>
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"> <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"bpederse@gmail.com"</span><span class="p">,</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">get_version</span><span class="p">(),</span></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python"> <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cmdclass</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extension</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"> <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python"> <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'cyvcf2'</span><span class="p">,</span> <span class="s" style="color: #d14;">'cyvcf2.tests'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">entry_points</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">console_scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -91,7 +98,7 @@ setup(</td>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"> <span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"> <span class="n" style="color: #333;">test_suite</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nose.collector'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"> <span class="n" style="color: #333;">tests_require</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'nose'</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p">],</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"> <span class="n" style="color: #333;">install_requires</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'numpy'</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'coloredlogs'</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">'click'</span></span><span class="p">],</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"> <span class="n" style="color: #333;">include_package_data</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"> <span class="n" style="color: #333;">zip_safe</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"><span class="p">)</span></span></pre>
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