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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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<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d">90ed00e3</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-05-02T12:02:51+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.30.15</pre>
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<h4>4 changed files:</h4>
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<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.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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<a href="#fd11e2e4bd1b8903c21cf95e681058bd017b76b9">
cyvcf2/tests/test_reader.py
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># v0.30.15</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"><span class="p">+</span> fix num_unknown when gts012=True (#236)</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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1
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># v0.30.14</span></span>
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2
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="p">+</span> use warnings instead of sys.stderr (#229 from @grahamgower)</span>
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3
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">+</span> use libdeflate in wheel build (#231 from @grahamgower)</span>
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<li id="2fbcc692367300b0691462028f2e5f9bcaaf0945">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d#2fbcc692367300b0691462028f2e5f9bcaaf0945"><strong>cyvcf2/__init__.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,</td>
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.1<span class="idiff left right deletion">4</span>"</span></span></pre></td>
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5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.30.1<span class="idiff left right addition">5</span>"</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d#164dc8610052ecd4fe73493df7bd8d4346cc2aa4"><strong>cyvcf2/cyvcf2.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1274" 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="1274" 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">@@ -1274,9 +1274,9 @@ cdef class Variant(object):</td>
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1274
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1274
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1274" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_types</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NULL</span><span class="p">:</span></span>
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1275
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1275
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1275" class="line" lang="cython"> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">gt_types</span></span>
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1276
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1276
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1276" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1277" 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">
1277
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1277" class="line" lang="cython"> <span class="k" style="font-weight: 600;">cdef</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">unknown</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">3</span> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">gts012</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">2</span></span>
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1277
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1278
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1278" class="line" lang="cython"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">vcf</span><span class="p">.</span><span class="n" style="color: #333;">n_samples</span><span class="p">):</span></span>
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1278
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<td class="new_line diff-line-num old" data-linenumber="1279" 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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1278" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_gt_types</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">:</span></span>
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1279
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC1279" class="line" lang="cython"> <span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">+=</span><span class="mi" style="color: #099;">1</span></span>
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1279
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1279" class="line" lang="cython"> <span class="n" style="color: #333;">n</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;">_gt_types</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">unknown</span><span class="p">)</span></span>
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1280
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1280
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1280" class="line" lang="cython"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">n</span></span>
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1281
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1281
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1281" class="line" lang="cython"></span>
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1282
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1282
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1282" class="line" lang="cython"> <span class="nb" style="color: #0086b3;">property</span> <span class="n" style="color: #333;">FORMAT</span><span class="p">:</span></span>
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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/90ed00e3b986178d008be642b1ea8ff357e2af1d#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">@@ -1302,3 +1302,17 @@ def test_genotypes():</td>
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1302
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1302
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1302" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="c1" style="color: #998; font-style: italic;"># only 0'th item</span></span>
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1303
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1303
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1303" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"i:"</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="s" style="color: #d14;">" a:"</span><span class="p">,</span> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span><span class="p">.</span><span class="n" style="color: #333;">array</span><span class="p">()[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="s" style="color: #d14;">" exp:"</span><span class="p">,</span> <span class="n" style="color: #333;">exp_array</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span></span>
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1304
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1304
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1304" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="p">(</span><span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">exp_array</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]).</span><span class="nb" style="color: #0086b3;">all</span><span class="p">(),</span> <span class="s" style="color: #d14;">" error with array"</span></span>
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1305
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1305" class="line" lang="python"></span>
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1306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1306" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_issue236</span><span class="p">():</span></span>
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1307
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1308
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1309
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1309" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">strict_gt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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1310
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1310" class="line" lang="python"> <span class="n" style="color: #333;">res</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[],</span> <span class="p">[]]</span></span>
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1311
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1312
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1312" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">gts</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="bp" style="color: #999;">True</span><span class="p">):</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1313" 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">
1313
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1313" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">HERE</span><span class="p">,</span> <span class="s" style="color: #d14;">"test-genotypes.vcf"</span><span class="p">),</span> <span class="n" style="color: #333;">gts012</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gts</span><span class="p">,</span> <span class="n" style="color: #333;">strict_gt</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">strict_gt</span><span class="p">)</span></span>
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1314
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1314" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">vcf</span><span class="p">:</span></span>
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1315
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1315" class="line" lang="python"> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">gts</span><span class="p">)].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">num_unknown</span><span class="p">)</span></span>
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1316
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<td class="new_line diff-line-num new" data-linenumber="1317" 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">
1317
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1317" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">res</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>
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<td class="new_line diff-line-num new" data-linenumber="1318" 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">
1318
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1318" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">res</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="mi" style="color: #099;">0</span></span></pre></td>
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