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 + [variantutils.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 _transform_to_gvcf_record(variant):
"""Modifies a variant to include gVCF allele and associated likelihoods.
Args:
variant: third_party.nucleus.protos.Variant. The Variant
to modify.
Returns:
The variant after applying the modification to its alleles and
allele-related FORMAT fields.
"""
if variantutils.GVCF_ALT_ALLELE not in variant.alternate_bases:
variant.alternate_bases.append(variantutils.GVCF_ALT_ALLELE)
# Add one new GL for het allele/gVCF for each of the other alleles, plus one
# for the homozygous gVCF allele.
num_new_gls = len(variant.alternate_bases) + 1
variant.calls[0].genotype_likelihood.extend([_GVCF_ALT_ALLELE_GL] *
num_new_gls)
if variant.calls[0].info and 'AD' in variant.calls[0].info:
variant.calls[0].info['AD'].values.extend(
[struct_pb2.Value(number_value=0)])
if variant.calls[0].info and 'VAF' in variant.calls[0].info:
variant.calls[0].info['VAF'].values.extend(
[struct_pb2.Value(number_value=0)])
return variant
def format_one(value):
if isinstance(value, str):
return struct_pb2.Value(string_value=value)
elif isinstance(value, (float, int)):
return struct_pb2.Value(number_value=value)
else:
raise ValueError('Unsupported type ', value)
def _format_test_variant(alleles, call_infos):
variant = test_utils.make_variant(chrom='20', start=0, alleles=alleles)
for i, call_info in enumerate(call_infos):
call = variant.calls.add(call_set_name='sample' + str(i))
for key, value in call_info.iteritems():
if not isinstance(value, (list, tuple)):
value = [value]
call.info[key].values.extend(
[struct_pb2.Value(number_value=v) for v in value])
return variant
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 set_variantcall_gq(variant_call, gq):
if 'GQ' in variant_call.info:
del variant_call.info['GQ']
variant_call.info['GQ'].values.extend([struct_pb2.Value(number_value=gq)])