class_docstr: Class for writing to native VCF files.
  
  Most users will want VcfWriter, which will write to either native VCF
  files or TFRecords files, based on the output filename's extensions.
class_docstr_tok: ["Class","for","writing","to","native","VCF","files",".","Most","users","will","want","VcfWriter",",","which","will","write","to","either","native","VCF","files","or","TFRecords","files",",","based","on","the","output","filename","'s","extensions","."]
docstr: Initializer for NativeVcfWriter.
  
  Args:
    output_path: str. The path to which to write the VCF file.
    header: nucleus.genomics.v1.VcfHeader. The header that defines all
      information germane to the constituent variants. This includes contigs,
      FILTER fields, INFO fields, FORMAT fields, samples, and all other
      structured and unstructured header lines.
    round_qualities: bool. If True, the QUAL field is rounded to one point
      past the decimal.
    excluded_info_fields: list(str). A list of INFO field IDs that should not
      be written to the output. If None, all INFO fields are included.
    excluded_format_fields: list(str). A list of FORMAT field IDs that should
      not be written to the output. If None, all FORMAT fields are included.
    retrieve_gl_and_pl_from_info_map: bool. If True, the "GL" and "PL" FORMAT
      fields are retrieved from the VariantCall.info map rather than from the
      top-level value in the VariantCall.genotype_likelihood field.
    exclude_header: bool. If True, write a headerless VCF.
docstr_tok: ["Initializer","for","NativeVcfWriter",".","Args",":","output_path",":","str",".","The","path","to","which","to","write","the","VCF","file",".","header",":","nucleus.genomics.v1.VcfHeader",".","The","header","that","defines","all","information","germane","to","the","constituent","variants",".","This","includes","contigs",",","FILTER","fields",",","INFO","fields",",","FORMAT","fields",",","samples",",","and","all","other","structured","and","unstructured","header","lines",".","round_qualities",":","bool",".","If","True",",","the","QUAL","field","is","rounded","to","one","point","past","the","decimal",".","excluded_info_fields",":","list","(","str",")",".","A","list","of","INFO","field","IDs","that","should","not","be","written","to","the","output",".","If","None",",","all","INFO","fields","are","included",".","excluded_format_fields",":","list","(","str",")",".","A","list","of","FORMAT","field","IDs","that","should","not","be","written","to","the","output",".","If","None",",","all","FORMAT","fields","are","included",".","retrieve_gl_and_pl_from_info_map",":","bool",".","If","True",",","the","``","GL","''","and","``","PL","''","FORMAT","fields","are","retrieved","from","the","VariantCall.info","map","rather","than","from","the","top-level","value","in","the","VariantCall.genotype_likelihood","field",".","exclude_header",":","bool",".","If","True",",","write","a","headerless","VCF","."]
code: def __init__(
      self,
      output_path,
      header=None,
      round_qualities=False,
      excluded_info_fields=None,
      excluded_format_fields=None,
      retrieve_gl_and_pl_from_info_map=False,
      exclude_header=False,
  ):
      """Initializer for NativeVcfWriter.
  
      Args:
        output_path: str. The path to which to write the VCF file.
        header: nucleus.genomics.v1.VcfHeader. The header that defines all
          information germane to the constituent variants. This includes contigs,
          FILTER fields, INFO fields, FORMAT fields, samples, and all other
          structured and unstructured header lines.
        round_qualities: bool. If True, the QUAL field is rounded to one point
          past the decimal.
        excluded_info_fields: list(str). A list of INFO field IDs that should not
          be written to the output. If None, all INFO fields are included.
        excluded_format_fields: list(str). A list of FORMAT field IDs that should
          not be written to the output. If None, all FORMAT fields are included.
        retrieve_gl_and_pl_from_info_map: bool. If True, the "GL" and "PL" FORMAT
          fields are retrieved from the VariantCall.info map rather than from the
          top-level value in the VariantCall.genotype_likelihood field.
        exclude_header: bool. If True, write a headerless VCF.
      """
      super(NativeVcfWriter, self).__init__()
  
      if header is None:
          header = variants_pb2.VcfHeader()
      writer_options = variants_pb2.VcfWriterOptions(
          round_qual_values=round_qualities,
          excluded_info_fields=excluded_info_fields,
          excluded_format_fields=excluded_format_fields,
          retrieve_gl_and_pl_from_info_map=retrieve_gl_and_pl_from_info_map,
          exclude_header=exclude_header,
      )
      self._writer = vcf_writer.VcfWriter.to_file(
          output_path, header, writer_options
      )
      self.field_access_cache = VcfHeaderCache(header)
  
imports: from __future__ import absolute_import
  from __future__ import division
  from __future__ import print_function
  from third_party.nucleus.io import genomics_reader
  from third_party.nucleus.io import genomics_writer
  from third_party.nucleus.io.python import vcf_reader
  from third_party.nucleus.io.python import vcf_writer
  from third_party.nucleus.protos import variants_pb2
  from third_party.nucleus.util import ranges
  from third_party.nucleus.util import variant_utils
  from third_party.nucleus.util import vcf_constants
label_desc: Use image node_id 1 to create a new NativeVcfWriter object from inherited base classes: genomics_writer with example: obj = NativeVcfWriter(output_path, header, round_qualities, excluded_info_fields, excluded_format_fields, retrieve_gl_and_pl_from_info_map, exclude_header)