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   <div class="section" id="module-apache_beam.io.vcfio">
 <span id="apache-beam-io-vcfio-module"></span><h1>apache_beam.io.vcfio module<a class="headerlink" href="#module-apache_beam.io.vcfio" title="Permalink to this headline">¶</a></h1>
 <p>A source for reading from VCF files (version 4.x).</p>
 <p>The 4.2 spec is available at <a class="reference external" href="https://samtools.github.io/hts-specs/VCFv4.2.pdf">https://samtools.github.io/hts-specs/VCFv4.2.pdf</a>.</p>
 <dl class="class">
 <dt id="apache_beam.io.vcfio.VariantInfo">
 <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">VariantInfo</code><span class="sig-paren">(</span><em>data</em>, <em>field_count</em><span class="sig-paren">)</span><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></p>
 <p>Create new instance of VariantInfo(data, field_count)</p>
 <dl class="attribute">
 <dt id="apache_beam.io.vcfio.VariantInfo.data">
 <code class="descname">data</code><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo.data" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>

 <dl class="attribute">
 <dt id="apache_beam.io.vcfio.VariantInfo.field_count">
 <code class="descname">field_count</code><a class="headerlink" href="#apache_beam.io.vcfio.VariantInfo.field_count" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>

 </dd></dl>

 <dl class="class">
 <dt id="apache_beam.io.vcfio.MalformedVcfRecord">
 <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">MalformedVcfRecord</code><span class="sig-paren">(</span><em>file_name</em>, <em>line</em><span class="sig-paren">)</span><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">tuple</span></code></p>
 <p>Create new instance of MalformedVcfRecord(file_name, line)</p>
 <dl class="attribute">
 <dt id="apache_beam.io.vcfio.MalformedVcfRecord.file_name">
 <code class="descname">file_name</code><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord.file_name" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 0</p>
 </dd></dl>

 <dl class="attribute">
 <dt id="apache_beam.io.vcfio.MalformedVcfRecord.line">
 <code class="descname">line</code><a class="headerlink" href="#apache_beam.io.vcfio.MalformedVcfRecord.line" title="Permalink to this definition">¶</a></dt>
 <dd><p>Alias for field number 1</p>
 </dd></dl>

 </dd></dl>

 <dl class="class">
 <dt id="apache_beam.io.vcfio.Variant">
 <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">Variant</code><span class="sig-paren">(</span><em>reference_name=None</em>, <em>start=None</em>, <em>end=None</em>, <em>reference_bases=None</em>, <em>alternate_bases=None</em>, <em>names=None</em>, <em>quality=None</em>, <em>filters=None</em>, <em>info=None</em>, <em>calls=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#Variant"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.Variant" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">future.types.newobject.newobject</span></code></p>
 <p>A class to store info about a genomic variant.</p>
 <p>Each object corresponds to a single record in a VCF file.</p>
 <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal"><span class="pre">Variant</span></code></a> object.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>reference_name</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The reference on which this variant occurs
 (such as <cite>chr20</cite> or <cite>X</cite>). .</li>
 <li><strong>start</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The position at which this variant occurs (0-based).
 Corresponds to the first base of the string of reference bases.</li>
 <li><strong>end</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a>) – The end position (0-based) of this variant. Corresponds to the
 first base after the last base in the reference allele.</li>
 <li><strong>reference_bases</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The reference bases for this variant.</li>
 <li><strong>alternate_bases</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a><em>]</em>) – The bases that appear instead of the
 reference bases.</li>
 <li><strong>names</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a><em>]</em>) – Names for the variant, for example a RefSNP ID.</li>
 <li><strong>quality</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#float" title="(in Python v2.7)"><em>float</em></a>) – Phred-scaled quality score (-10log10 prob(call is wrong))
 Higher values imply better quality.</li>
 <li><strong>filters</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a><em>]</em>) – A list of filters (normally quality filters) this
 variant has failed. <cite>PASS</cite> indicates this variant has passed all
 filters.</li>
 <li><strong>info</strong> (<a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)"><em>dict</em></a>) – A map of additional variant information. The key is specified
 in the VCF record and the value is of type <code class="docutils literal"><span class="pre">VariantInfo</span></code>.</li>
 <li><strong>calls</strong> (list of <a class="reference internal" href="#apache_beam.io.vcfio.VariantCall" title="apache_beam.io.vcfio.VariantCall"><code class="xref py py-class docutils literal"><span class="pre">VariantCall</span></code></a>) – The variant calls for this variant.
 Each one represents the determination of genotype with respect to this
 variant.</li>
 </ul>
 </td>
 </tr>
 </tbody>
 </table>
 </dd></dl>

 <dl class="class">
 <dt id="apache_beam.io.vcfio.VariantCall">
 <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">VariantCall</code><span class="sig-paren">(</span><em>name=None</em>, <em>genotype=None</em>, <em>phaseset=None</em>, <em>info=None</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#VariantCall"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.VariantCall" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <code class="xref py py-class docutils literal"><span class="pre">future.types.newobject.newobject</span></code></p>
 <p>A class to store info about a variant call.</p>
 <p>A call represents the determination of genotype with respect to a particular
 variant. It may include associated information such as quality and phasing.</p>
 <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.VariantCall" title="apache_beam.io.vcfio.VariantCall"><code class="xref py py-class docutils literal"><span class="pre">VariantCall</span></code></a> object.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>name</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The name of the call.</li>
 <li><strong>genotype</strong> (<em>List</em><em>[</em><a class="reference external" href="https://docs.python.org/2/library/functions.html#int" title="(in Python v2.7)"><em>int</em></a><em>]</em>) – The genotype of this variant call as specified by
 the VCF schema. The values are either <cite>0</cite> representing the reference,
 or a 1-based index into alternate bases. Ordering is only important if
 <cite>phaseset</cite> is present. If a genotype is not called (that is, a <cite>.</cite> is
 present in the GT string), -1 is used</li>
 <li><strong>phaseset</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – If this field is present, this variant call’s genotype
 ordering implies the phase of the bases and is consistent with any other
 variant calls in the same reference sequence which have the same
 phaseset value. If the genotype data was phased but no phase set was
 specified, this field will be set to <cite>*</cite>.</li>
 <li><strong>info</strong> (<a class="reference external" href="https://docs.python.org/2/library/stdtypes.html#dict" title="(in Python v2.7)"><em>dict</em></a>) – A map of additional variant call information. The key is
 specified in the VCF record and the type of the value is specified by
 the VCF header FORMAT.</li>
 </ul>
 </td>
 </tr>
 </tbody>
 </table>
 </dd></dl>

 <dl class="class">
 <dt id="apache_beam.io.vcfio.ReadFromVcf">
 <em class="property">class </em><code class="descclassname">apache_beam.io.vcfio.</code><code class="descname">ReadFromVcf</code><span class="sig-paren">(</span><em>file_pattern=None</em>, <em>compression_type='auto'</em>, <em>validate=True</em>, <em>allow_malformed_records=False</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#ReadFromVcf"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.ReadFromVcf" title="Permalink to this definition">¶</a></dt>
 <dd><p>Bases: <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal"><span class="pre">apache_beam.transforms.ptransform.PTransform</span></code></a></p>
 <p>A <a class="reference internal" href="apache_beam.transforms.ptransform.html#apache_beam.transforms.ptransform.PTransform" title="apache_beam.transforms.ptransform.PTransform"><code class="xref py py-class docutils literal"><span class="pre">PTransform</span></code></a> for reading VCF
 files.</p>
 <p>Parses VCF files (version 4) using PyVCF library. If file_pattern specifies
 multiple files, then the header from each file is used separately to parse
 the content. However, the output will be a PCollection of
 <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal"><span class="pre">Variant</span></code></a> (or <a class="reference internal" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="apache_beam.io.vcfio.MalformedVcfRecord"><code class="xref py py-class docutils literal"><span class="pre">MalformedVcfRecord</span></code></a> for failed reads) objects.</p>
 <p>Initialize the <a class="reference internal" href="#apache_beam.io.vcfio.ReadFromVcf" title="apache_beam.io.vcfio.ReadFromVcf"><code class="xref py py-class docutils literal"><span class="pre">ReadFromVcf</span></code></a> transform.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>file_pattern</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – The file path to read from either as a single file or
 a glob pattern.</li>
 <li><strong>compression_type</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#str" title="(in Python v2.7)"><em>str</em></a>) – Used to handle compressed input files.
 Typical value is <a class="reference internal" href="apache_beam.io.filesystem.html#apache_beam.io.filesystem.CompressionTypes.AUTO" title="apache_beam.io.filesystem.CompressionTypes.AUTO"><code class="xref py py-attr docutils literal"><span class="pre">CompressionTypes.AUTO</span></code></a>, in which case the
 underlying file_path’s extension will be used to detect the compression.</li>
 <li><strong>validate</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – flag to verify that the files exist during the pipeline
 creation time.</li>
 <li><strong>allow_malformed_records</strong> (<a class="reference external" href="https://docs.python.org/2/library/functions.html#bool" title="(in Python v2.7)"><em>bool</em></a>) – determines if failed VCF
 record reads will be tolerated. Failed record reads will result in a
 <a class="reference internal" href="#apache_beam.io.vcfio.MalformedVcfRecord" title="apache_beam.io.vcfio.MalformedVcfRecord"><code class="xref py py-class docutils literal"><span class="pre">MalformedVcfRecord</span></code></a> being returned from the read of the record
 rather than a <a class="reference internal" href="#apache_beam.io.vcfio.Variant" title="apache_beam.io.vcfio.Variant"><code class="xref py py-class docutils literal"><span class="pre">Variant</span></code></a>.</li>
 </ul>
 </td>
 </tr>
 </tbody>
 </table>
 <dl class="method">
 <dt id="apache_beam.io.vcfio.ReadFromVcf.expand">
 <code class="descname">expand</code><span class="sig-paren">(</span><em>pvalue</em><span class="sig-paren">)</span><a class="reference internal" href="_modules/apache_beam/io/vcfio.html#ReadFromVcf.expand"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#apache_beam.io.vcfio.ReadFromVcf.expand" title="Permalink to this definition">¶</a></dt>
 <dd></dd></dl>

 </dd></dl>

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