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)