def _make_labeler_from_options(self): truth_vcf_reader = vcf.VcfReader( self.options.truth_variants_filename, excluded_format_fields=['GL', 'GQ', 'PL']) confident_regions = read_confident_regions(self.options) if (self.options.labeler_algorithm == deepvariant_pb2.DeepVariantOptions.POSITIONAL_LABELER): return positional_labeler.PositionalVariantLabeler( truth_vcf_reader=truth_vcf_reader, confident_regions=confident_regions) elif (self.options.labeler_algorithm == deepvariant_pb2.DeepVariantOptions.HAPLOTYPE_LABELER): return haplotype_labeler.HaplotypeLabeler( truth_vcf_reader=truth_vcf_reader, ref_reader=self.ref_reader, confident_regions=confident_regions) else: raise ValueError('Unexpected labeler_algorithm', self.options.labeler_algorithm)
def _make_labeler_from_options(self): """Creates the labeler from options.""" truth_vcf_reader = vcf.VcfReader( self.options.truth_variants_filename, excluded_format_fields=['GL', 'GQ', 'PL']) confident_regions = read_confident_regions(self.options) if (self.options.labeler_algorithm == deepvariant_pb2.DeepVariantOptions.POSITIONAL_LABELER): return positional_labeler.PositionalVariantLabeler( truth_vcf_reader=truth_vcf_reader, confident_regions=confident_regions) elif (self.options.labeler_algorithm == deepvariant_pb2.DeepVariantOptions.HAPLOTYPE_LABELER): return haplotype_labeler.HaplotypeLabeler( truth_vcf_reader=truth_vcf_reader, ref_reader=self.ref_reader, confident_regions=confident_regions) elif (self.options.labeler_algorithm == deepvariant_pb2.DeepVariantOptions.CUSTOMIZED_CLASSES_LABELER): if (not FLAGS.customized_classes_labeler_classes_list or not FLAGS.customized_classes_labeler_info_field_name): raise ValueError( 'For -labeler_algorithm=customized_classes_labeler, ' 'you need to set ' '-customized_classes_labeler_classes_list and ' '-customized_classes_labeler_info_field_name.') return customized_classes_labeler.CustomizedClassesVariantLabeler( truth_vcf_reader=truth_vcf_reader, confident_regions=confident_regions, classes_list=FLAGS.customized_classes_labeler_classes_list, info_field_name=FLAGS. customized_classes_labeler_info_field_name) else: raise ValueError('Unexpected labeler_algorithm', self.options.labeler_algorithm)
def _make_labeler(self, variants, confident_regions): return positional_labeler.PositionalVariantLabeler( truth_vcf_reader=vcf.InMemoryVcfReader(variants), confident_regions=confident_regions)