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<h3>
Nilesh Patra pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cyvcf2">Debian Med / cyvcf2</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/eba05721427c97ef0d5184f6ef356bd599351c0d">eba05721</a></strong>
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<span>by Nilesh Patra</span>
<i>at 2020-09-28T22:44:39+05:30</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.20.7</pre>
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<h4>3 changed files:</h4>
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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="2fbcc692367300b0691462028f2e5f9bcaaf0945">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/eba05721427c97ef0d5184f6ef356bd599351c0d#2fbcc692367300b0691462028f2e5f9bcaaf0945"><strong>cyvcf2/__init__.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@ from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"> <span class="n" style="color: #333;">par_het</span><span class="p">)</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">Reader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCFReader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">VCF</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.20.<span class="idiff left right">6</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.20.<span class="idiff left right">7</span>"</span></span></pre>
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<li id="164dc8610052ecd4fe73493df7bd8d4346cc2aa4">
<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/eba05721427c97ef0d5184f6ef356bd599351c0d#164dc8610052ecd4fe73493df7bd8d4346cc2aa4"><strong>cyvcf2/cyvcf2.pyx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1029" 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="1029" 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">@@ -1029,17 +1029,24 @@ cdef class Genotypes(object):</td>
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1029
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1029
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<pre style="margin: 0;"> <span id="LC1029" class="line" lang="cython"><span class="s" style="color: #d14;"> array returns an int16 numpy array of shape n_samples, (ploidy + 1).</span></span>
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1030
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1030
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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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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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<pre style="margin: 0;">+<span id="LC1032" class="line" lang="cython"><span class="s" style="color: #d14;"> Unknown alleles are represented by -1 and mixed-ploidy arrays</span></span>
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<pre style="margin: 0;">+<span id="LC1033" class="line" lang="cython"><span class="s" style="color: #d14;"> are padded with -2 to indicate non-alleles.</span></span>
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1032
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1034
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<pre style="margin: 0;"> <span id="LC1034" class="line" lang="cython"><span class="s" style="color: #d14;"> """</span></span>
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1033
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<pre style="margin: 0;"> <span id="LC1035" 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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1034
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1036
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<pre style="margin: 0;"> <span id="LC1036" 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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1037
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<pre style="margin: 0;"> <span id="LC1037" class="line" lang="cython"></span>
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1038
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<pre style="margin: 0;">+<span id="LC1038" 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;">raw</span></span>
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1036
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1039
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<pre style="margin: 0;"> <span id="LC1039" 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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1040
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<pre style="margin: 0;"> <span id="LC1040" 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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1041
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<pre style="margin: 0;"> <span id="LC1041" 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;">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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1039
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1042
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<pre style="margin: 0;"> <span id="LC1042" class="line" lang="cython"></span>
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1040
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1043
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<pre style="margin: 0;"> <span id="LC1043" 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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1041
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<td class="diff-line-num new_line" data-linenumber="1044" 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">
1044
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<pre style="margin: 0;"> <span id="LC1044" 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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1042
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<td class="diff-line-num new_line old" data-linenumber="1045" 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="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> <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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1045
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<pre style="margin: 0;">+<span id="LC1045" class="line" lang="cython"> <span class="n" style="color: #333;">raw</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;">_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>
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<td class="diff-line-num new new_line" data-linenumber="1046" 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">
1046
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<pre style="margin: 0;">+<span id="LC1046" class="line" lang="cython"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">raw</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">bcf_int32_vector_end</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1047" 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">
1047
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<pre style="margin: 0;">+<span id="LC1047" 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> <span class="n" style="color: #333;">allele</span><span class="p">]</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>
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<td class="diff-line-num new new_line" data-linenumber="1048" 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">
1048
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<pre style="margin: 0;">+<span id="LC1048" class="line" lang="cython"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1049" 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">
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 class="p">[</span><span class="n" style="color: #333;">ind</span><span class="p">,</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="n" style="color: #333;">raw</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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1043
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1050
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<pre style="margin: 0;"> <span id="LC1050" 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> <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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1044
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1051
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<pre style="margin: 0;"> <span id="LC1051" class="line" lang="cython"></span>
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1045
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1052
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<pre style="margin: 0;"> <span id="LC1052" 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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<a href="https://salsa.debian.org/med-team/cyvcf2/-/commit/eba05721427c97ef0d5184f6ef356bd599351c0d#fd11e2e4bd1b8903c21cf95e681058bd017b76b9"><strong>cyvcf2/tests/test_reader.py</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="808" 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">@@ -808,6 +808,38 @@ def test_access_genotype():</td>
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808
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808
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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python"> <span class="n" style="color: #333;">v</span><span class="p">.</span><span class="n" style="color: #333;">genotype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">gts</span></span>
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809
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809
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<pre style="margin: 0;"> <span id="LC809" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span> <span class="s" style="color: #d14;">"1/0:6728,1:F 0/1:22,1:G"</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span></span>
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810
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810
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<pre style="margin: 0;"> <span id="LC810" class="line" lang="python"></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_access_genotype_array</span><span class="p">():</span></span>
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812
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<pre style="margin: 0;">+<span id="LC812" 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="LC813" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="python"><span class="s" style="color: #d14;">7 55086956 . C G 0 . . GT:ADP_ALL:RULE 0/0:6728,1:F 1|1:22,1:G</span></span>
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="python"><span class="s" style="color: #d14;">7 55086957 . T A,C,G 0 . . GT:ADP_ALL:RULE 1/2:6768,2,2,1:F2,F3,F4 2|3:1,2,3,4:G2,G3,G4</span></span>
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="python"><span class="s" style="color: #d14;">7 55086958 . T G 0 . . GT:ADP_ALL:RULE 0/1/.:6768,2,2,1:F2,F3,F4 0:1,2,3,4:G2,G3,G4</span></span>
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="python"><span class="s" style="color: #d14;">7 55086959 . T G,T 0 . . GT:ADP_ALL:RULE . 0|2:1,2,3,4:G2,G3,G4</span></span>
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">+<span id="LC820" 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="LC821" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">testing</span><span class="p">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="python"> <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="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]],</span> <span class="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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<pre style="margin: 0;">+<span id="LC824" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC826" 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="LC827" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">testing</span><span class="p">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="python"> <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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]],</span> <span class="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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<pre style="margin: 0;">+<span id="LC830" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC832" 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="LC833" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">testing</span><span class="p">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="python"> <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="mi" style="color: #099;">0</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="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">],</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;">2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int16</span><span class="p">)</span></span>
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836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="python"> <span class="p">)</span></span>
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837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"></span>
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838
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<pre style="margin: 0;">+<span id="LC838" 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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839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="python"> <span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">testing</span><span class="p">.</span><span class="n" style="color: #333;">assert_array_equal</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"> <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>
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="python"> <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="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;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">]],</span> <span class="n" style="color: #333;">dtype</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">int16</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="python"> <span class="p">)</span></span>
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843
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<pre style="margin: 0;"> <span id="LC843" class="line" lang="python"></span>
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844
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<pre style="margin: 0;"> <span id="LC844" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_alt_homozygous_gt</span><span class="p">():</span></span>
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845
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<pre style="margin: 0;"> <span id="LC845" 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-multiallelic-homozygous-alt.vcf.gz"</span><span class="p">))</span></span>
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