def test_transform_to_gvcf_add_allele(self, prior_alts, prior_gls, prior_vaf):
variant = _create_variant(
ref_name='chr1',
start=10,
ref_base='A',
alt_bases=prior_alts,
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=prior_gls)
prior_vaf_values = [struct_pb2.Value(number_value=v) for v in prior_vaf]
variant.calls[0].info['VAF'].values.extend(prior_vaf_values)
expected = _create_variant(
ref_name='chr1',
start=10,
ref_base='A',
alt_bases=prior_alts + [vcf_constants.GVCF_ALT_ALLELE],
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=prior_gls + ([postprocess_variants._GVCF_ALT_ALLELE_GL] *
(len(prior_alts) + 2)))
expected.calls[0].info['VAF'].values.extend(
prior_vaf_values + [struct_pb2.Value(number_value=0)])
actual = postprocess_variants._transform_to_gvcf_record(variant)
self.assertEqual(actual, expected)
def test_transform_to_gvcf_add_allele(self, prior_alts, prior_gls, prior_vaf):
variant = _create_variant(
ref_name='chr1',
start=10,
ref_base='A',
alt_bases=prior_alts,
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=prior_gls)
prior_vaf_values = [struct_pb2.Value(number_value=v) for v in prior_vaf]
variant.calls[0].info['VAF'].values.extend(prior_vaf_values)
expected = _create_variant(
ref_name='chr1',
start=10,
ref_base='A',
alt_bases=prior_alts + [vcf_constants.GVCF_ALT_ALLELE],
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=prior_gls + ([postprocess_variants._GVCF_ALT_ALLELE_GL] *
(len(prior_alts) + 2)))
expected.calls[0].info['VAF'].values.extend(
prior_vaf_values + [struct_pb2.Value(number_value=0)])
actual = postprocess_variants._transform_to_gvcf_record(variant)
self.assertEqual(actual, expected)
def test_transform_to_gvcf_no_allele_addition(self, alts, gls, vaf):
variant = _create_variant(ref_name='chr1',
start=10,
ref_base='A',
alt_bases=alts,
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=gls)
vaf_values = [struct_pb2.Value(number_value=v) for v in vaf]
variant.calls[0].info['VAF'].values.extend(vaf_values)
expected = variants_pb2.Variant()
expected.CopyFrom(variant)
actual = postprocess_variants._transform_to_gvcf_record(variant)
self.assertEqual(actual, expected)
def test_transform_to_gvcf_no_allele_addition(self, alts, gls, vaf):
variant = _create_variant(
ref_name='chr1',
start=10,
ref_base='A',
alt_bases=alts,
qual=40,
filter_field='PASS',
genotype=[0, 1],
gq=None,
likelihoods=gls)
vaf_values = [struct_pb2.Value(number_value=v) for v in vaf]
variant.calls[0].info['VAF'].values.extend(vaf_values)
expected = variants_pb2.Variant()
expected.CopyFrom(variant)
actual = postprocess_variants._transform_to_gvcf_record(variant)
self.assertEqual(actual, expected)