def test_genotype_as_alleles_raises_with_bad_inputs(self):
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(None)
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(test_utils.make_variant(gt=None))
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(
test_utils.make_variant(alleles=['A', 'C'], gt=[0, 0]), call_ix=1)
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
def test_genotype_as_alleles_raises_with_bad_inputs(self):
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(None)
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(test_utils.make_variant(gt=None))
with self.assertRaises(Exception):
variant_utils.genotype_as_alleles(
test_utils.make_variant(alleles=['A', 'C'], gt=[0, 0]), call_ix=1)
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
def compute_filter_fields(variant, min_quality):
"""Computes the filter fields for this variant.
Variant filters are generated based on its quality score value and particular
genotype call.
Args:
variant: Variant to filter.
min_quality: Minimum acceptable phred scaled variant detection probability.
Returns:
Filter field strings to be added to the variant.
"""
if variant_utils.genotype_type(variant) == variant_utils.GenotypeType.hom_ref:
return [dv_vcf_constants.DEEP_VARIANT_REF_FILTER]
elif variant.quality < min_quality:
return [dv_vcf_constants.DEEP_VARIANT_QUAL_FILTER]
else:
return [dv_vcf_constants.DEEP_VARIANT_PASS]
def compute_filter_fields(variant, min_quality):
"""Computes the filter fields for this variant.
Variant filters are generated based on its quality score value and particular
genotype call.
Args:
variant: Variant to filter.
min_quality: Minimum acceptable phred scaled variant detection probability.
Returns:
Filter field strings to be added to the variant.
"""
if variant_utils.genotype_type(variant) == variant_utils.GenotypeType.hom_ref:
return [dv_vcf_constants.DEEP_VARIANT_REF_FILTER]
elif variant.quality < min_quality:
return [dv_vcf_constants.DEEP_VARIANT_QUAL_FILTER]
else:
return [dv_vcf_constants.DEEP_VARIANT_PASS]
def test_genotype_type_raises_with_bad_args(self):
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
def test_genotype_type(self, variant, expected): self.assertEqual(variant_utils.genotype_type(variant), expected)
def test_genotype_type_raises_with_bad_args(self):
with self.assertRaises(Exception):
variant_utils.genotype_type(None)
def test_genotype_type(self, variant, expected): self.assertEqual(variant_utils.genotype_type(variant), expected)
