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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc">df085d3c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-09-18T08:19:49+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.20.6</pre>
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<h4>7 changed files:</h4>
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<a href="#2fbcc692367300b0691462028f2e5f9bcaaf0945">
cyvcf2/__init__.py
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<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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<a href="#cd30d32bf3321852047e22f38ce5e9348e3e4226">
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+
cyvcf2/tests/test_writer.py
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<a href="#62df078594b947ca6f787a59ae6ddefabce9fcad">
docs/source/index.rst
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<a href="#dfb7aae9e4b7c56de453e2fb3727950ea41f4ea6">
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docs/source/writing.rst
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,8 @@ cyvcf2</td>
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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="err" style="color: #a61717; background-color: #e3d2d2;">0.20.0</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="err" style="color: #a61717; background-color: #e3d2d2;">1.10.</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">The latest documentation for cyvcf2 can be found here:</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" 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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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown">If you use cyvcf2, please cite the <span class="p">[</span><span class="nv" style="color: #008080;">paper</span><span class="p">](</span><span class="sx" style="color: #d14;">https://academic.oup.com/bioinformatics/article/2971439/cyvcf2</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="86" 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="88" 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">@@ -86,6 +88,7 @@ autoconf</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">make</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown">cd ..</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">pip install -r requirements.txt</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">CYTHONIZE=1 pip install -e .</span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>
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<li id="2fbcc692367300b0691462028f2e5f9bcaaf0945">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc#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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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="n" style="color: #333;">par_het</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCFReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.20.<span class="idiff left right">1</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.20.<span class="idiff left right">6</span>"</span></span></pre>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;">#cython: profile=False</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;">#cython:language_level=3</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cython"><span class="c1" style="color: #998; font-style: italic;">#cython: embedsignature=True</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cython"><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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="154" 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="155" 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">@@ -154,27 +155,19 @@ cdef class HTSFile:</td>
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154
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<pre style="margin: 0;"> <span id="LC155" 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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156
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<pre style="margin: 0;"> <span id="LC156" 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="LC157" 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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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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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cython"> <span class="n" style="color: #333;">writing</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">b"w"</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="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="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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">writing</span><span class="p">:</span></span>
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158
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<pre style="margin: 0;"> <span id="LC160" 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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<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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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 old old_line" data-linenumber="162" 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">
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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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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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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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cython"></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="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="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 old_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">
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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="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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165
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<td class="diff-line-num new_line" data-linenumber="164" 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">
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;">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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<td class="diff-line-num new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;"> <span id="LC165" 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 old_line" data-linenumber="167" 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">
167
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<td class="diff-line-num new_line" data-linenumber="166" 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">
166
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<pre style="margin: 0;"> <span id="LC166" 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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<td class="diff-line-num new_line old" data-linenumber="167" 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="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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169
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<td class="diff-line-num new_line old" data-linenumber="167" 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="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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170
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<td class="diff-line-num new_line old" data-linenumber="167" 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="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 old old_line" data-linenumber="171" 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">
171
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<td class="diff-line-num new_line old" data-linenumber="167" 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="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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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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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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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cython"></span>
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174
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<td class="diff-line-num new_line" data-linenumber="168" 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">
168
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<pre style="margin: 0;"> <span id="LC168" 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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175
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># from a file descriptor</span></span>
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176
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<td class="diff-line-num new_line" data-linenumber="170" 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">
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="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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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 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">
178
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171
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<pre style="margin: 0;"> <span id="LC171" 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 old_line" data-linenumber="179" 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">
179
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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;">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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180
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<td class="diff-line-num new_line" data-linenumber="173" 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">
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;">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 unfold js-unfold old_line" data-linenumber="182" 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="175" 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">@@ -182,7 +175,6 @@ cdef class HTSFile:</td>
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<td class="diff-line-num old_line" data-linenumber="182" 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">
182
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<td class="diff-line-num new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;"> <span id="LC175" 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 old_line" data-linenumber="183" 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">
183
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<td class="diff-line-num new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;"> <span id="LC176" 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 old_line" data-linenumber="184" 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">
184
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<td class="diff-line-num new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;"> <span id="LC177" 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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185
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<td class="diff-line-num new_line old" data-linenumber="178" 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="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 old_line" data-linenumber="186" 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">
186
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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="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 old_line" data-linenumber="187" 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">
187
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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 old_line" data-linenumber="188" 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">
188
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180
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<pre style="margin: 0;"> <span id="LC180" 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 unfold js-unfold old_line" data-linenumber="304" 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="296" 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">@@ -304,6 +296,9 @@ cdef class VCF(HTSFile):</td>
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304
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<td class="diff-line-num new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;"> <span id="LC296" 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_hdr_sync</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 old_line" data-linenumber="305" 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">
305
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<td class="diff-line-num new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</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="306" 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">
306
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<td class="diff-line-num new_line" data-linenumber="298" 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">
298
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<pre style="margin: 0;"> <span id="LC298" 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 add '%s' to header"</span><span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="307" 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="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"##contig"</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="cython"> <span class="c1" style="color: #998; font-style: italic;"># need to trigger a refresh of seqnames</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_seqnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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307
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302
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span></span>
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308
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<td class="diff-line-num new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cython"></span>
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<td class="diff-line-num old_line" data-linenumber="309" 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">
309
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<td class="diff-line-num new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">add_info_to_header</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">adict</span><span class="p">):</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="382" 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="377" 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">@@ -382,6 +377,11 @@ cdef class VCF(HTSFile):</td>
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382
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<td class="diff-line-num new_line" data-linenumber="377" 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">
377
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<pre style="margin: 0;"> <span id="LC377" 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;">"unable to update to header"</span><span class="p">)</span></span>
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383
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cython"></span>
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384
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<td class="diff-line-num new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_index</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">index_path</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 new new_line" data-linenumber="380" 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">
380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index_path</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;">".tbi"</span><span class="p">):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="385" 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="381" 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">
381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">idx</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="nf" style="color: #900; font-weight: 600;">to_bytes</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="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">index_path</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
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<pre style="margin: 0;">+<span id="LC382" 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;">idx</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="383" 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">
383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span></span>
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<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cython"></span>
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385
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<td class="diff-line-num new_line" data-linenumber="385" 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">
385
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<pre style="margin: 0;"> <span id="LC385" 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;">hts_idx_load2</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">to_bytes</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="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">index_path</span><span class="p">))</span></span>
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<td class="diff-line-num old_line" data-linenumber="386" 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">
386
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<td class="diff-line-num new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;"> <span id="LC386" 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="387" 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">
387
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<td class="diff-line-num new_line" data-linenumber="387" 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">
387
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">idx</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="nf" style="color: #900; font-weight: 600;">to_bytes</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="nf" style="color: #900; font-weight: 600;">to_bytes</span><span class="p">(</span><span class="n" style="color: #333;">index_path</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="579" 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="579" 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">@@ -579,11 +579,15 @@ cdef class VCF(HTSFile):</td>
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579
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<td class="diff-line-num new_line" data-linenumber="579" 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">
579
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<pre style="margin: 0;"> <span id="LC579" class="line" lang="cython"> <span class="k" style="font-weight: 600;">with</span> <span class="k" style="font-weight: 600;">nogil</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="580" 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">
580
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<td class="diff-line-num new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cython"> <span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_init</span><span class="p">()</span></span>
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<td class="diff-line-num old_line" data-linenumber="581" 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">
581
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<td class="diff-line-num new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;"> <span id="LC581" 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_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 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;">b</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="582" 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">
582
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<td class="diff-line-num new_line old" data-linenumber="582" 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="LC582" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</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 new old_line" data-linenumber="583" 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="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="idiff left"> </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">b</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">errcode</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">BCF_ERR_CTG_UNDEF</span></span><span class="p">:</span></span>
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583
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<td class="diff-line-num new_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">
583
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">newVariant</span><span class="p">(</span><span class="n" style="color: #333;">b</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 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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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC584" 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 old_line" data-linenumber="585" 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">
585
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<td class="diff-line-num new_line" data-linenumber="585" 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">
585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">bcf_destroy</span><span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="586" 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">
586
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<td class="diff-line-num new_line old" data-linenumber="586" 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="cython"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">StopIteration</span></span>
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<td class="diff-line-num new old_line" data-linenumber="587" 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="586" 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">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</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 class="c1" style="color: #998; font-style: italic;"># end-of-file</span></span>
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<pre style="margin: 0;">+<span id="LC587" 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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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>
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<pre style="margin: 0;">+<span id="LC589" 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 parsing variant with `htslib::bcf_read` error-code: %d"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="p">.</span><span class="n" style="color: #333;">errcode</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">samples</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cython"> <span class="s" style="color: #d14;">"list of samples pulled from the VCF."</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">@@ -1026,9 +1030,8 @@ cdef class Genotypes(object):</td>
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1026
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<pre style="margin: 0;"> <span id="LC1030" class="line" lang="cython"><span class="s" style="color: #d14;"> The last column indicates phased (1 is phased, 0 is unphased).</span></span>
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1027
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1031
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<pre style="margin: 0;"> <span id="LC1031" class="line" lang="cython"><span class="s" style="color: #d14;"> The other columns indicate the alleles, e.g. [0, 1, 1] is 0|1.</span></span>
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1028
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1032
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<pre style="margin: 0;"> <span id="LC1032" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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1029
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<pre style="margin: 0;">-<span id="LC1029" 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;">int16_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">to_return</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;">int16_t</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="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int16_t</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC1030" class="line" lang="cython"> <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;">n_samples</span></span>
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1031
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<pre style="margin: 0;">-<span id="LC1031" class="line" lang="cython"> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><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="mi" style="color: #099;">1</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC1033" 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="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int16_t</span><span class="p">,</span> <span class="n" style="color: #333;">ndim</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="n" style="color: #333;">to_return</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;">n_samples</span><span class="p">,</span> <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="mi" style="color: #099;">1</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC1034" class="line" lang="cython"> <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;">int16</span><span class="p">)</span></span>
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1035
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<pre style="margin: 0;"> <span id="LC1035" class="line" lang="cython"></span>
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1036
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<pre style="margin: 0;"> <span id="LC1036" 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;">ind</span></span>
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1037
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<pre style="margin: 0;"> <span id="LC1037" 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;">allele</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">@@ -1036,18 +1039,10 @@ cdef class Genotypes(object):</td>
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1039
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<pre style="margin: 0;"> <span id="LC1039" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC1040" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ind</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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1038
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<td class="diff-line-num new_line" data-linenumber="1041" 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">
1041
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<pre style="margin: 0;"> <span id="LC1041" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">allele</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;">ploidy</span><span class="p">):</span></span>
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1039
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<td class="diff-line-num new_line old" data-linenumber="1042" 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="LC1039" class="line" lang="cython"> <span class="n" style="color: #333;">to_return</span><span class="p">[</span><span class="n" style="color: #333;">ind</span><span class="idiff left"> </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">p</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span> <span class="n" style="color: #333;">allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_raw</span><span class="p">[</span><span class="n" style="color: #333;">ind</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;">ploidy</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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1040
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<td class="diff-line-num new_line old" data-linenumber="1042" 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="LC1040" class="line" lang="cython"> <span class="n" style="color: #333;">to_return</span><span class="p">[</span><span class="n" style="color: #333;">ind</span><span class="idiff left"> </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">p</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ploidy</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_raw</span><span class="p">[</span><span class="n" style="color: #333;">ind</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;">ploidy</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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1042
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<pre style="margin: 0;">+<span id="LC1042" class="line" lang="cython"> <span class="n" style="color: #333;">to_return</span><span class="p">[</span><span class="n" style="color: #333;">ind</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_raw</span><span class="p">[</span><span class="n" style="color: #333;">ind</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;">ploidy</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">allele</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>></span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1043" 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">
1043
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<pre style="margin: 0;">+<span id="LC1043" class="line" lang="cython"> <span class="n" style="color: #333;">to_return</span><span class="p">[</span><span class="n" style="color: #333;">ind</span><span class="p"><span class="idiff left right">,</span></span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">ploidy</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_raw</span><span class="p">[</span><span class="n" style="color: #333;">ind</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;">ploidy</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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1041
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1044
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<pre style="margin: 0;"> <span id="LC1044" class="line" lang="cython"></span>
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1042
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<pre style="margin: 0;">-<span id="LC1042" 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;">2</span><span class="p">]</span></span>
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1043
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<pre style="margin: 0;">-<span id="LC1043" 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="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span></span>
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1044
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<pre style="margin: 0;">-<span id="LC1044" 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;">1</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;">ploidy</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>
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1045
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<pre style="margin: 0;">-<span id="LC1045" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">PyArray_SimpleNewFromData</span><span class="p">(</span></span>
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1046
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<pre style="margin: 0;">-<span id="LC1046" class="line" lang="cython"> <span class="mi" style="color: #099;">2</span><span class="p">,</span></span>
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1047
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<pre style="margin: 0;">-<span id="LC1047" class="line" lang="cython"> <span class="n" style="color: #333;">shape</span><span class="p">,</span></span>
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1048
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<pre style="margin: 0;">-<span id="LC1048" class="line" lang="cython"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">NPY_INT16</span><span class="p">,</span></span>
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1049
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<pre style="margin: 0;">-<span id="LC1049" class="line" lang="cython"> <span class="n" style="color: #333;">to_return</span></span>
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<pre style="margin: 0;">-<span id="LC1050" class="line" lang="cython"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">to_return</span></span>
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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="cython"></span>
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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</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;">int</span> <span class="n" style="color: #333;">i</span><span class="p">):</span></span>
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1053
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1048
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<pre style="margin: 0;"> <span id="LC1048" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;">## return the Allele objects for the i'th sample.</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">@@ -1434,20 +1429,32 @@ cdef class Variant(object):</td>
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1434
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1429
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<pre style="margin: 0;"> <span id="LC1429" class="line" lang="cython"></span>
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1435
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1430
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<pre style="margin: 0;"> <span id="LC1430" 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="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">float32_t</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;">"c"</span><span class="p">]</span> <span class="n" style="color: #333;">afloat</span></span>
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1436
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1431
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<pre style="margin: 0;"> <span id="LC1431" 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="p">[</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int32_t</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;">"c"</span><span class="p">]</span> <span class="n" style="color: #333;">aint</span></span>
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1432
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<pre style="margin: 0;">+<span id="LC1432" 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;">bytesp</span></span>
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1437
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1433
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<pre style="margin: 0;"> <span id="LC1433" class="line" lang="cython"></span>
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1438
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<pre style="margin: 0;">-<span id="LC1438" 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;">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;">0</span><span class="p">]</span></span>
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1439
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<pre style="margin: 0;">-<span id="LC1439" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">((</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">object</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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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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1441
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<pre style="margin: 0;">-<span id="LC1441" class="line" lang="cython"></span>
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1434
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<pre style="margin: 0;">+<span id="LC1434" 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;">size</span></span>
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1442
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1435
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<pre style="margin: 0;"> <span id="LC1435" 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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1443
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1436
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<pre style="margin: 0;"> <span id="LC1436" 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;">signedinteger</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</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;">unsignedinteger</span><span class="p">):</span></span>
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1437
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<pre style="margin: 0;">+<span id="LC1437" 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;">0</span><span class="p">]</span></span>
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1438
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<pre style="margin: 0;">+<span id="LC1438" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">((</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">object</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1439
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<pre style="margin: 0;">+<span id="LC1439" 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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1444
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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;">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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1445
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<pre style="margin: 0;"> <span id="LC1441" 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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1442
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<pre style="margin: 0;"> <span id="LC1442" 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;">floating</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="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;">0</span><span class="p">]</span></span>
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1444
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<pre style="margin: 0;">+<span id="LC1444" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">((</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">object</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="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>
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1445
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<pre style="margin: 0;">+<span id="LC1445" 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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1447
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1446
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<pre style="margin: 0;"> <span id="LC1446" 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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1448
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1447
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<pre style="margin: 0;"> <span id="LC1447" 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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1448
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<pre style="margin: 0;">+<span id="LC1448" 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;">bytes_</span><span class="p">):</span></span>
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1449
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<pre style="margin: 0;">+<span id="LC1449" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">((</span><span class="o" style="font-weight: 600;"><</span><span class="nb" style="color: #0086b3;">object</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="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 new new_line" data-linenumber="1450" 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">
1450
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<pre style="margin: 0;">+<span id="LC1450" 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;">"Setting string type format fields with number>1 are currently not supported"</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1451" 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">
1451
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<pre style="margin: 0;">+<span id="LC1451" 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;">data</span><span class="p">.</span><span class="n" style="color: #333;">flags</span><span class="p">[</span><span class="s" style="color: #d14;">'C_CONTIGUOUS'</span><span class="p">]:</span></span>
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1452
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<pre style="margin: 0;">+<span id="LC1452" class="line" lang="cython"> <span class="n" style="color: #333;">data</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;">ascontiguousarray</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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1453
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<pre style="margin: 0;">+<span id="LC1453" 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;">nbytes</span></span>
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1454
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<pre style="margin: 0;">+<span id="LC1454" class="line" lang="cython"> <span class="n" style="color: #333;">bytesp</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">char</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;">data</span></span>
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<pre style="margin: 0;">+<span id="LC1455" 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</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="n" style="color: #333;">bytesp</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">BCF_HT_STR</span><span class="p">)</span></span>
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1449
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<td class="diff-line-num new_line" data-linenumber="1456" 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">
1456
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<pre style="margin: 0;"> <span id="LC1456" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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1450
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<pre style="margin: 0;">-<span id="LC1450" 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;">"format: currently only float<span class="idiff left right"> and int</span> numpy arrays are supported. got %s"</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>
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<pre style="margin: 0;">+<span id="LC1457" 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;">"format: currently only float<span class="idiff left right">, int and string (fixed length ASCII np.bytes_)</span> numpy arrays are supported. got %s"</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>
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1451
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1458
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<pre style="margin: 0;"> <span id="LC1458" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</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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1452
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1459
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<pre style="margin: 0;"> <span id="LC1459" 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 (%d) setting format with: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">ret</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">data</span><span class="p">[:</span><span class="mi" style="color: #099;">100</span><span class="p">]))</span></span>
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1453
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1460
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<pre style="margin: 0;"> <span id="LC1460" 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">@@ -1845,10 +1852,22 @@ cdef class Variant(object):</td>
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1845
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1852
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<pre style="margin: 0;"> <span id="LC1852" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">get</span><span class="p">(</span><span class="s" style="color: #d14;">b'SVTYPE'</span><span class="p">)</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>
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1846
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1853
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<pre style="margin: 0;"> <span id="LC1853" class="line" lang="cython"></span>
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1847
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1854
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<pre style="margin: 0;"> <span id="LC1854" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">CHROM</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1848" 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">
1848
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<td class="diff-line-num new_line old" data-linenumber="1855" 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="LC1848" class="line" lang="cython"> <span class="s" style="color: #d14;">"<span class="idiff left right">chromosome of the variant.</span>"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1855" 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">
1855
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<pre style="margin: 0;">+<span id="LC1855" class="line" lang="cython"> <span class="s" style="color: #d14;">"<span class="idiff left right">""Chromosome of the variant.""</span>"</span></span>
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1849
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1856
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<pre style="margin: 0;"> <span id="LC1856" 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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1850
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1857
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<pre style="margin: 0;"> <span id="LC1857" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_id2name</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="n" style="color: #333;">rid</span><span class="p">).</span><span class="nf" style="color: #900; font-weight: 600;">decode</span><span class="p">()</span></span>
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1851
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1858
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<pre style="margin: 0;"> <span id="LC1858" class="line" lang="cython"></span>
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1859
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<pre style="margin: 0;">+<span id="LC1859" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__set__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">new_chrom</span><span class="p">):</span></span>
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1860
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<pre style="margin: 0;">+<span id="LC1860" class="line" lang="cython"> <span class="n" style="color: #333;">new_rid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_id2int</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="n" style="color: #333;">BCF_DT_CTG</span><span class="p">,</span> <span class="n" style="color: #333;">new_chrom</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1861" 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">
1861
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<pre style="margin: 0;">+<span id="LC1861" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_rid</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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1862
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<pre style="margin: 0;">+<span id="LC1862" class="line" lang="cython"> <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="nf" style="color: #900; font-weight: 600;">add_to_header</span><span class="p">(</span><span class="s" style="color: #d14;">"##contig=<ID={}>"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">new_chrom</span><span class="p">))</span></span>
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1863
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<pre style="margin: 0;">+<span id="LC1863" class="line" lang="cython"> <span class="n" style="color: #333;">new_rid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_id2int</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="n" style="color: #333;">BCF_DT_CTG</span><span class="p">,</span> <span class="n" style="color: #333;">new_chrom</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">encode</span><span class="p">())</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1864" 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">
1864
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<pre style="margin: 0;">+<span id="LC1864" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">new_rid</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 new old_line" data-linenumber="1852" 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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1865
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<pre style="margin: 0;">+<span id="LC1865" class="line" lang="cython"> <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;">"Unable to add {} to CHROM"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">new_chrom</span><span class="p">))</span></span>
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1866
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<pre style="margin: 0;">+<span id="LC1866" class="line" lang="cython"> <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="nf" style="color: #900; font-weight: 600;">write</span><span class="p">(</span></span>
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1867
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<pre style="margin: 0;">+<span id="LC1867" class="line" lang="cython"> <span class="s" style="color: #d14;">"[cyvcf2]: added new contig {} to header"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">new_chrom</span><span class="p">)</span></span>
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1868
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<pre style="margin: 0;">+<span id="LC1868" class="line" lang="cython"> <span class="p">)</span></span>
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1869
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<pre style="margin: 0;">+<span id="LC1869" class="line" lang="cython"> <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;">rid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_rid</span></span>
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1870
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<pre style="margin: 0;">+<span id="LC1870" class="line" lang="cython"></span>
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1852
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1871
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<pre style="margin: 0;"> <span id="LC1871" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">var_type</span><span class="p">:</span></span>
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1853
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1872
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<pre style="margin: 0;"> <span id="LC1872" class="line" lang="cython"> <span class="s" style="color: #d14;">"type of variant (snp/indel/sv)"</span></span>
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1854
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1873
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<pre style="margin: 0;"> <span id="LC1873" 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="1913" 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="1932" 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">@@ -1913,7 +1932,7 @@ cdef class Variant(object):</td>
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1913
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1932
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<pre style="margin: 0;"> <span id="LC1932" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">FILTER</span><span class="p">:</span></span>
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1914
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1933
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<pre style="margin: 0;"> <span id="LC1933" class="line" lang="cython"> <span class="s" style="color: #d14;">"""the value of FILTER from the VCF field.</span></span>
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1915
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1934
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<pre style="margin: 0;"> <span id="LC1934" class="line" lang="cython"></span>
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1916
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<pre style="margin: 0;">-<span id="LC1916" class="line" lang="cython"><span class="s" style="color: #d14;"> a value of PASS in the VCF will give None for this function</span></span>
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1935
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<pre style="margin: 0;">+<span id="LC1935" class="line" lang="cython"><span class="s" style="color: #d14;"> a value of PASS <span class="idiff left right">or '.' </span>in the VCF will give None for this function</span></span>
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1917
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1936
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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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1918
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1937
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<pre style="margin: 0;"> <span id="LC1937" 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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1919
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1938
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<pre style="margin: 0;"> <span id="LC1938" 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>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2047" 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="2066" 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">@@ -2047,7 +2066,8 @@ cdef class INFO(object):</td>
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2047
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2066
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<pre style="margin: 0;"> <span id="LC2066" class="line" lang="cython"></span>
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2048
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2067
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<pre style="margin: 0;"> <span id="LC2067" 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_info_flag</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="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;">key</span><span class="p">),</span> <span class="s" style="color: #d14;">b""</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">))</span></span>
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2049
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<td class="diff-line-num new_line" data-linenumber="2068" 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">
2068
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<pre style="margin: 0;"> <span id="LC2068" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ret</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="2050" 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">
2050
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<pre style="margin: 0;">-<span id="LC2050" 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;">"not able to set flag"</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span><span class="p">)</span></span>
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2069
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<pre style="margin: 0;">+<span id="LC2069" 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;">"not able to set: %s -> %s (%d)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">ret</span><span class="p">))</span></span>
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2070
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<pre style="margin: 0;">+<span id="LC2070" class="line" lang="cython"></span>
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2051
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2071
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<pre style="margin: 0;"> <span id="LC2071" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span></span>
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2052
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2072
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<pre style="margin: 0;"> <span id="LC2072" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">iint</span></span>
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2053
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2073
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<pre style="margin: 0;"> <span id="LC2073" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">ifloat</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">@@ -2225,6 +2245,22 @@ cdef class Writer(VCF):</td>
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2225
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2245
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<pre style="margin: 0;"> <span id="LC2245" class="line" lang="cython"><span class="s" style="color: #d14;"> path to file</span></span>
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2226
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2246
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<pre style="margin: 0;"> <span id="LC2246" class="line" lang="cython"><span class="s" style="color: #d14;"> tmpl: VCF</span></span>
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2227
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2247
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<pre style="margin: 0;"> <span id="LC2247" class="line" lang="cython"><span class="s" style="color: #d14;"> a template to use to create the output header.</span></span>
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2248
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<pre style="margin: 0;">+<span id="LC2248" class="line" lang="cython"><span class="s" style="color: #d14;"> mode: str</span></span>
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2249
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<pre style="margin: 0;">+<span id="LC2249" class="line" lang="cython"><span class="s" style="color: #d14;"> | Mode to use for writing the file. If ``None`` (default) is given, the mode is</span></span>
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2250
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<pre style="margin: 0;">+<span id="LC2250" class="line" lang="cython"><span class="s" style="color: #d14;"> inferred from the filename extension. If stdout (``"-"``) is provided for ``fname``</span></span>
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2251
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<pre style="margin: 0;">+<span id="LC2251" class="line" lang="cython"><span class="s" style="color: #d14;"> and ``mode`` is left at default, uncompressed VCF will be produced.</span></span>
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2252
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<pre style="margin: 0;">+<span id="LC2252" class="line" lang="cython"><span class="s" style="color: #d14;"> | Valid values are:</span></span>
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2253
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<pre style="margin: 0;">+<span id="LC2253" class="line" lang="cython"><span class="s" style="color: #d14;"> | - ``"wbu"``: uncompressed BCF</span></span>
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2254
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<pre style="margin: 0;">+<span id="LC2254" class="line" lang="cython"><span class="s" style="color: #d14;"> | - ``"wb"``: compressed BCF</span></span>
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2255
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<pre style="margin: 0;">+<span id="LC2255" class="line" lang="cython"><span class="s" style="color: #d14;"> | - ``"wz"``: compressed VCF</span></span>
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2256
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<pre style="margin: 0;">+<span id="LC2256" class="line" lang="cython"><span class="s" style="color: #d14;"> | - ``"w"``: uncompressed VCF</span></span>
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2257
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<pre style="margin: 0;">+<span id="LC2257" class="line" lang="cython"><span class="s" style="color: #d14;"> | Compression level can also be indicated by adding a single integer to one of</span></span>
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2258
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<pre style="margin: 0;">+<span id="LC2258" class="line" lang="cython"><span class="s" style="color: #d14;"> the compressed modes (e.g. ``"wz4"`` for VCF with compressions level 4).</span></span>
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2259
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<pre style="margin: 0;">+<span id="LC2259" class="line" lang="cython"></span>
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2260
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<pre style="margin: 0;">+<span id="LC2260" class="line" lang="cython"><span class="s" style="color: #d14;"> Note</span></span>
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2261
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<pre style="margin: 0;">+<span id="LC2261" class="line" lang="cython"><span class="s" style="color: #d14;"> ----</span></span>
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2262
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<pre style="margin: 0;">+<span id="LC2262" class="line" lang="cython"><span class="s" style="color: #d14;"> File extensions ``.bcf`` and ``.bcf.gz`` will both return compressed BCF. If you</span></span>
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2263
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<pre style="margin: 0;">+<span id="LC2263" class="line" lang="cython"><span class="s" style="color: #d14;"> want uncompressed BCF you must explicitly provide the appropriate ``mode``.</span></span>
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2228
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2264
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<pre style="margin: 0;"> <span id="LC2264" class="line" lang="cython"></span>
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2229
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2265
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<pre style="margin: 0;"> <span id="LC2265" class="line" lang="cython"><span class="s" style="color: #d14;"> Returns</span></span>
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2230
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2266
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<pre style="margin: 0;"> <span id="LC2266" class="line" lang="cython"><span class="s" style="color: #d14;"> -------</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2272" 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">@@ -2236,7 +2272,8 @@ cdef class Writer(VCF):</td>
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2236
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2272
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<pre style="margin: 0;"> <span id="LC2272" 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;">header_written</span></span>
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2237
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2273
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<pre style="margin: 0;"> <span id="LC2273" 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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2238
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2274
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<pre style="margin: 0;"> <span id="LC2274" class="line" lang="cython"></span>
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2239
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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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2275
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<pre style="margin: 0;">+<span id="LC2275" 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="bp" style="color: #999;">None</span><span class="p">):</span></span>
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2276
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<pre style="margin: 0;">+<span id="LC2276" class="line" lang="cython"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">_infer_file_mode</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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2240
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2277
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<pre style="margin: 0;"> <span id="LC2277" 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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2241
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2278
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<pre style="margin: 0;"> <span id="LC2278" 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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2242
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2279
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<pre style="margin: 0;"> <span id="LC2279" 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 unfold js-unfold old_line" data-linenumber="2244" 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="2281" 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">@@ -2244,6 +2281,28 @@ cdef class Writer(VCF):</td>
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2244
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2281
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<pre style="margin: 0;"> <span id="LC2281" class="line" lang="cython"> <span class="nf" style="color: #900; font-weight: 600;">bcf_hdr_sync</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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2245
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2282
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<pre style="margin: 0;"> <span id="LC2282" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">header_written</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>
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2246
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2283
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<pre style="margin: 0;"> <span id="LC2283" class="line" lang="cython"></span>
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2284
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<pre style="margin: 0;">+<span id="LC2284" class="line" lang="cython"> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">staticmethod</span></span>
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2285
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<pre style="margin: 0;">+<span id="LC2285" class="line" lang="cython"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_infer_file_mode</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="bp" style="color: #999;">None</span><span class="p">):</span></span>
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2286
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<pre style="margin: 0;">+<span id="LC2286" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mode</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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2287
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<pre style="margin: 0;">+<span id="LC2287" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mode</span></span>
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2288
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<pre style="margin: 0;">+<span id="LC2288" class="line" lang="cython"></span>
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<td class="diff-line-num new new_line" data-linenumber="2289" 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">
2289
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<pre style="margin: 0;">+<span id="LC2289" class="line" lang="cython"> <span class="n" style="color: #333;">from_path</span> <span class="o" style="font-weight: 600;">=</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="2290" 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">
2290
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<pre style="margin: 0;">+<span id="LC2290" 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;">from_path</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2291" 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">
2291
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<pre style="margin: 0;">+<span id="LC2291" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"w"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2292" 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">
2292
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<pre style="margin: 0;">+<span id="LC2292" class="line" lang="cython"></span>
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<td class="diff-line-num new new_line" data-linenumber="2293" 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">
2293
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<pre style="margin: 0;">+<span id="LC2293" class="line" lang="cython"> <span class="n" style="color: #333;">fname</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="2294" 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">
2294
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<pre style="margin: 0;">+<span id="LC2294" class="line" lang="cython"> <span class="n" style="color: #333;">is_compressed</span> <span class="o" style="font-weight: 600;">=</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>
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<td class="diff-line-num new new_line" data-linenumber="2295" 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">
2295
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<pre style="margin: 0;">+<span id="LC2295" class="line" lang="cython"> <span class="n" style="color: #333;">fmt_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_compressed</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2296" 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">
2296
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<pre style="margin: 0;">+<span id="LC2296" class="line" lang="cython"> <span class="n" style="color: #333;">file_fmt</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fname</span><span class="p">.</span><span class="nf" style="color: #900; font-weight: 600;">split</span><span class="p">(</span><span class="s" style="color: #d14;">"."</span><span class="p">)[</span><span class="n" style="color: #333;">fmt_idx</span><span class="p">]</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2297" 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">
2297
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<pre style="margin: 0;">+<span id="LC2297" class="line" lang="cython"> <span class="c1" style="color: #998; font-style: italic;"># bcftools output write mode chars - https://github.com/samtools/bcftools/blob/76392b3014de70b7fa5c6b5c9d5bc47361951770/version.c#L64-L70</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2298" 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">
2298
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<pre style="margin: 0;">+<span id="LC2298" class="line" lang="cython"> <span class="n" style="color: #333;">inferred_mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2299" 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">
2299
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<pre style="margin: 0;">+<span id="LC2299" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_fmt</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"bcf"</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2300" 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">
2300
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<pre style="margin: 0;">+<span id="LC2300" class="line" lang="cython"> <span class="n" style="color: #333;">inferred_mode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"b"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2301" 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">
2301
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<pre style="margin: 0;">+<span id="LC2301" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_compressed</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">file_fmt</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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<td class="diff-line-num new new_line" data-linenumber="2302" 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">
2302
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<pre style="margin: 0;">+<span id="LC2302" class="line" lang="cython"> <span class="n" style="color: #333;">inferred_mode</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"z"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2303" 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">
2303
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<pre style="margin: 0;">+<span id="LC2303" class="line" lang="cython"></span>
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<td class="diff-line-num new new_line" data-linenumber="2304" 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">
2304
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<pre style="margin: 0;">+<span id="LC2304" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">inferred_mode</span></span>
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<td class="diff-line-num new new_line" data-linenumber="2305" 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">
2305
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<pre style="margin: 0;">+<span id="LC2305" class="line" lang="cython"></span>
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2247
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2306
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<pre style="margin: 0;"> <span id="LC2306" 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="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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2307
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<pre style="margin: 0;"> <span id="LC2307" 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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2249
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2308
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<pre style="margin: 0;"> <span id="LC2308" 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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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc#fd11e2e4bd1b8903c21cf95e681058bd017b76b9"><strong>cyvcf2/tests/test_reader.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">@@ -67,18 +67,6 @@ def test_format_str():</td>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">f</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 class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"RULE"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="p">[</span><span class="s" style="color: #d14;">'F2,F3,F4'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G2,G3,G4'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="python"><span class="s" style="color: #d14;">def test_write_format_str():</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="s" style="color: #d14;"> vcf = VCF(os.path.join(HERE, "test-format-string.vcf"))</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="python"><span class="s" style="color: #d14;"> wtr = Writer("x.vcf", vcf)</span></span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="s" style="color: #d14;"> variant = next(vcf)</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="python"><span class="s" style="color: #d14;"> variant.set_format("TSTRING", np.array(["asdfxx","35</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"]))</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"><span class="s" style="color: #d14;"> wtr.write_record(variant)</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="s" style="color: #d14;"> wtr.close()</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;"> assert "asdfxx" in str(variant), str(variant)</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;"> assert "35" in str(variant)</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_missing_samples</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'101976-101976'</span><span class="p">,</span> <span class="s" style="color: #d14;">'sample_not_in_vcf'</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC72" 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 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 class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">samples</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">@@ -669,6 +657,31 @@ def test_set_format_int3():</td>
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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">allclose</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">"P3"</span><span class="p">),</span> <span class="n" style="color: #333;">exp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC660" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_format_str_bytes_second_longer</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC661" 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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<pre style="margin: 0;">+<span id="LC662" 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;">"STR"</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;">"String"</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;">"String 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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<pre style="margin: 0;">+<span id="LC663" 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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<pre style="margin: 0;">+<span id="LC664" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC665" 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;">"STR"</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="s" style="color: #d14;">b'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'barbaz'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">'STR'</span><span class="p">)</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;">array</span><span class="p">([</span><span class="s" style="color: #d14;">'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">'barbaz'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_format_str_bytes_first_longer</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC669" 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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<pre style="margin: 0;">+<span id="LC670" 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;">"STR"</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;">"String"</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;">"String 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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<pre style="margin: 0;">+<span id="LC671" 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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<pre style="margin: 0;">+<span id="LC672" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC673" 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;">"STR"</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="s" style="color: #d14;">b'foobar'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'baz'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="s" style="color: #d14;">'STR'</span><span class="p">)</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;">array</span><span class="p">([</span><span class="s" style="color: #d14;">'foobar'</span><span class="p">,</span> <span class="s" style="color: #d14;">'baz'</span><span class="p">]))</span></span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_format_str_bytes_number3</span><span class="p">():</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Confirm currently not supported</span></span>
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<pre style="margin: 0;">+<span id="LC678" 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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<pre style="margin: 0;">+<span id="LC679" 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;">"STR"</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;">3</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;">"String"</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;">"String 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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680
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<pre style="margin: 0;">+<span id="LC680" 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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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="python"></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python"> <span class="n" style="color: #333;">contents</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;">array</span><span class="p">([[</span><span class="s" style="color: #d14;">b'foo'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'barbaz'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'biz'</span><span class="p">],</span> <span class="p">[</span><span class="s" style="color: #d14;">b'blub'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'bloop'</span><span class="p">,</span> <span class="s" style="color: #d14;">b'blop'</span><span class="p">]])</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="python"> <span class="n" style="color: #333;">assert_raises</span><span class="p">(</span><span class="nb" style="color: #0086b3;">Exception</span><span class="p">,</span> <span class="n" style="color: #333;">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;">"STR"</span><span class="p">,</span> <span class="n" style="color: #333;">contents</span><span class="p">)</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python"></span>
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_gts</span><span class="p">():</span></span>
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686
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<pre style="margin: 0;"> <span id="LC686" 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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687
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<pre style="margin: 0;"> <span id="LC687" 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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="881" 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="894" 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">@@ -881,6 +894,32 @@ def test_set_pos():</td>
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881
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894
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<pre style="margin: 0;"> <span id="LC894" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">start</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">22</span></span>
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882
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895
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<pre style="margin: 0;"> <span id="LC895" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">POS</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">23</span></span>
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883
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896
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<pre style="margin: 0;"> <span id="LC896" class="line" lang="python"></span>
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897
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<pre style="margin: 0;">+<span id="LC897" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_chrom_when_contig_not_in_header</span><span class="p">():</span></span>
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898
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<pre style="margin: 0;">+<span id="LC898" class="line" lang="python"> <span class="n" style="color: #333;">test_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{}/test-strict-gt-option-flag.vcf.gz'</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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899
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<pre style="margin: 0;">+<span id="LC899" class="line" lang="python"> <span class="n" style="color: #333;">new_chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NEW"</span></span>
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900
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<pre style="margin: 0;">+<span id="LC900" 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>
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901
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<pre style="margin: 0;">+<span id="LC901" class="line" lang="python"> <span class="n" style="color: #333;">original_seqnames</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;">seqnames</span></span>
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902
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<pre style="margin: 0;">+<span id="LC902" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">new_chrom</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">original_seqnames</span></span>
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<pre style="margin: 0;">+<span id="LC903" 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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904
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<pre style="margin: 0;">+<span id="LC904" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC905" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">CHROM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_chrom</span></span>
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906
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<pre style="margin: 0;">+<span id="LC906" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">CHROM</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">new_chrom</span></span>
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907
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<pre style="margin: 0;">+<span id="LC907" class="line" lang="python"> <span class="n" style="color: #333;">expected_seqnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">original_seqnames</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">new_chrom</span><span class="p">])</span></span>
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908
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<pre style="margin: 0;">+<span id="LC908" 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;">seqnames</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_seqnames</span></span>
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909
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<pre style="margin: 0;">+<span id="LC909" class="line" lang="python"></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_chrom_after_contig_is_added_to_header</span><span class="p">():</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="python"> <span class="n" style="color: #333;">test_vcf</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'{}/test-strict-gt-option-flag.vcf.gz'</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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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="python"> <span class="n" style="color: #333;">new_chrom</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NEW"</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" 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>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="python"> <span class="n" style="color: #333;">original_seqnames</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;">seqnames</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="python"> <span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">add_to_header</span><span class="p">(</span><span class="s" style="color: #d14;">"##contig=<ID={},length=15>"</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">new_chrom</span><span class="p">))</span></span>
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916
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<pre style="margin: 0;">+<span id="LC916" class="line" lang="python"> <span class="n" style="color: #333;">expected_seqnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">original_seqnames</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">[</span><span class="n" style="color: #333;">new_chrom</span><span class="p">])</span></span>
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917
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<pre style="margin: 0;">+<span id="LC917" 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;">seqnames</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected_seqnames</span></span>
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918
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<pre style="margin: 0;">+<span id="LC918" 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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919
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<pre style="margin: 0;">+<span id="LC919" class="line" lang="python"></span>
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920
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<pre style="margin: 0;">+<span id="LC920" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">CHROM</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_chrom</span></span>
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921
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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="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">CHROM</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">new_chrom</span></span>
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922
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<pre style="margin: 0;">+<span id="LC922" class="line" lang="python"></span>
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884
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923
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<pre style="margin: 0;"> <span id="LC923" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_set_qual</span><span class="p">():</span></span>
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924
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<pre style="margin: 0;"> <span id="LC924" 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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886
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925
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<pre style="margin: 0;"> <span id="LC925" 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;">v</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc#cd30d32bf3321852047e22f38ce5e9348e3e4226"><strong>cyvcf2/tests/test_writer.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;">io</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">StringIO</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"></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;">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;">Writer</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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" 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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7
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<pre style="margin: 0;">+<span id="LC7" 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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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;">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="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TestFileModeInference</span><span class="p">:</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithVcfFname_returnsUncompressedVcf</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.vcf"</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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15
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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;">actual</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;">_infer_file_mode</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="LC17" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></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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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithBcfFname_returnsCompressedBcf</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="LC22" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.bcf"</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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="LC26" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb"</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithBcfFnameAndUncompressedMode_returnsUncompressedBcf</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="LC31" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.bcf"</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wbu"</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="n" style="color: #333;">actual</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;">_infer_file_mode</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="LC35" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mode</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></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;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithCompressedBcfFname_returnsCompressedBcf</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="LC40" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.bcf.gz"</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</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 class="n" style="color: #333;">actual</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;">_infer_file_mode</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="LC44" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb"</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="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithCompressedVcfFname_returnsCompressedVcf</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="LC49" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.vcf.gz"</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wz"</span></span>
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54
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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 class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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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="LC57" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithStdOut_returnsUncompressedVcf</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"-"</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python"></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></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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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithNonVcfName_returnsUncompressedVcf</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="LC67" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"foo"</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;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="python"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithIntFname_returnsUncompressedVcf</span><span class="p">(</span><span class="bp" style="color: #999;">self</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;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</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;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"></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;">actual</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;">_infer_file_mode</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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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></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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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithHandle_returnsUncompressedVcf</span><span class="p">(</span><span class="bp" style="color: #999;">self</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="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">StringIO</span><span class="p">()</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="python"></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_defaultModeWithPosixPath_returnsUncompressedVcf</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="LC94" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="s" style="color: #d14;">"test.vcf"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"w"</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python"></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_explicitMode_doesNotInferFromFname</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="LC103" class="line" lang="python"> <span class="n" style="color: #333;">fname</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"test.vcf.gz"</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python"> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb4"</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python"> <span class="n" style="color: #333;">actual</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;">_infer_file_mode</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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python"> <span class="n" style="color: #333;">expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"wb4"</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">actual</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">expected</span></span></pre>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,10 +59,12 @@ See the :ref:`api` for detailed documentation, but the most common usage is summ</td>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">Modifying Existing Records</span>
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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">.. this example is also in the writing.rst page</span>
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<pre style="margin: 0;"> <span id="LC64" 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="LC65" class="line" lang="plaintext">However, it also offers some means of modifying existing VCFs. Here, we</span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">show an example of how to <span class="idiff left right">annotate variants with the genes that they overlap.</span></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">show an example of how to <span class="idiff left right">modify the INFO field at a locus to annotate</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">variants with the genes that they overlap.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;"> <span id="LC70" 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">@@ -88,6 +90,8 @@ 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="LC90" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"> w.close(); vcf.close()</span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">More info on writing vcfs can be found :doc:`here <writing>`</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">Setting Genotyping Strictness</span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext">=============================</span>
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<pre style="margin: 0;"> <span id="LC97" 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">@@ -133,13 +137,20 @@ Tests can be run with:</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext"> python setup.py test</span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">Known Limitations</span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">=================</span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">* `cyvcf2` currently does not support reading VCFs encoded with UTF-8 with non-ASCII characters in the contents of string-typed FORMAT fields.</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">For limitations on writing VCFs, see :ref:`here <Limitations with writing>`</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="plaintext">See Also</span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="plaintext">========</span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="plaintext">Pysam also <span class="idiff left right">[has a cython wrapper to htslib](https://github.com/pysam-developers/pysam/blob/master/pysam/cbcf.pyx)</span> and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.</span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">Pysam also <span class="idiff left right">`has a cython wrapper to htslib <https://github.com/pysam-developers/pysam/blob/master/pysam/cbcf.pyx>`_</span> and one block of code here is taken directly from that library. But, the optimizations that we want for gemini are very specific so we have chosen to create a separate project.</span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="plaintext">.. toctree::</span>
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<pre style="margin: 0;">-<span id="LC142" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">2</span></span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> :maxdepth: <span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="plaintext"> docstrings</span>
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> writing</span>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></span></pre>
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<li id="dfb7aae9e4b7c56de453e2fb3727950ea41f4ea6">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/df085d3c1b77df9c27e5ace4c1ad2c2bda066efc#dfb7aae9e4b7c56de453e2fb3727950ea41f4ea6"><strong>docs/source/writing.rst</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Modifying Existing VCFs</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=======================</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" 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="LC5" class="line" lang="plaintext">However, it also offers some means of modifying existing VCFs.</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Modifying the INFO field</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">------------------------</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">.. this is the same example as on the index.rst page</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Here, we show an example of how to modify the INFO field at a locus to annotate</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">variants with the genes that they overlap.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> from cyvcf2 import VCF, Writer</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> vcf = VCF(VCF_PATH)</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> # adjust the header to contain the new field</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> # the keys 'ID', 'Description', 'Type', and 'Number' are required.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> vcf.add_info_to_header({'ID': 'gene', 'Description': 'overlapping gene',</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> 'Type':'Character', 'Number': '1'})</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" 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="LC25" class="line" lang="plaintext"> fname = "out.vcf"</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> w = Writer(fname, vcf)</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> for v in vcf:</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> # The get_gene_intersections function is not shown.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> # This could be any operation to find intersections</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> # or any manipulation required by the user.</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> genes = get_gene_intersections(v)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> if genes is not None:</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> v.INFO["gene"] = ",".join(genes)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> w.write_record(v)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> w.close(); vcf.close()</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Modifying genotypes and the FORMAT field</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">----------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Here is an example where we filter some calls from records in a VCF. This demonstrates</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">how to add to the FORMAT field and how to modify genotypes at a locus.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">.. code-block:: python</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> from cyvcf2 import VCF, Writer</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> vcf = VCF(VCF_PATH)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> # adjust the header to contain the new field</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> # the keys 'ID', 'Description', 'Type', and 'Number' are required.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> vcf.add_format_to_header({</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> 'ID': 'FILTER_CODE',</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> 'Description': 'Numeric code for filtering reason',</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> 'Type': 'Integer',</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> 'Number': '1'</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> })</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC58" 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="LC59" class="line" lang="plaintext"> fname = "out.vcf"</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> w = Writer(fname, vcf)</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> for v in vcf:</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> # The filter_samples function is not shown.</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> # This could be any manipulation required by the user.</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> # Since we specified the FILTER_CODE format field is an Integer</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> # with Number=1, reasons must be an n x 1 numpy array of integers</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> # where n is the number of samples.</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> indicies, reasons = filter_samples(v)</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> if indicies:</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> # add the reasons array to the format dictionary at this locus</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> v.set_format('FILTER_CODE', reasons)</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> for index in indicies:</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> # overwrite the genotypes of each filtered locus to be nocalls</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> # Note: until the reassignment to v.genotypes below, this</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> # leaves the v Variant object in an inconsistent state</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> v.genotypes[index] = [-1]*v.ploidy + [False]</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> # it is necessary to reassign the genotypes field</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> # so that the v Variant object reprocess it and future calls</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> # to functions like v.genotype.array() properly reflect</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> # the changed genotypes</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> v.genotypes = v.genotypes</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> w.write_record(v)</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> w.close(); vcf.close()</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">.. _Limitations with writing:</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">Known Limitations with Writing VCFs</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">-----------------------------------</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">* `cyvcf2` currently does not support writing VCFs encoded with UTF-8 with non-ASCII characters in the contents of string-typed FORMAT fields.</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">* `cyvcf2` currently does not support writing string type format fields with number>1.</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"></span></pre>
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