def _get_variant_stats(variant, vaf_available=False, vcf_reader=None):
"""Returns a VariantStats object corresponding to the input variant."""
vtype = _get_variant_type(variant)
is_transition, is_transversion = _tstv(variant, vtype)
vaf = None
if vaf_available:
vaf = _get_vaf(variant, vcf_reader)
return VariantStats(
reference_name=variant.reference_name,
position=(variant.start + 1),
reference_bases=variant.reference_bases,
alternate_bases=list(variant.alternate_bases),
variant_type=vtype,
is_transition=is_transition,
is_transversion=is_transversion,
is_variant=variant_utils.is_variant_call(variant),
depth=variantcall_utils.get_format(
variant_utils.only_call(variant), 'DP'),
genotype_quality=variantcall_utils.get_gq(
variant_utils.only_call(variant)),
genotype=str(
sorted(variantcall_utils.get_gt(variant_utils.only_call(variant)))),
vaf=vaf,
qual=variant.quality)
def test_get_format(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_get_fn.return_value = (
functools.partial(
struct_utils.get_string_field, is_single_field=True))
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, 'GP', [.1, .2, .7])
variantcall_utils.set_format(call, 'AD', [55, 3])
variantcall_utils.set_format(call, 'DP', 58)
variantcall_utils.set_format(call, 'GL', [-1, -3, -5.5])
variantcall_utils.set_format(call, 'GT', [0, 1])
variantcall_utils.set_format(call, 'FT', ['LowQual'])
actual = variantcall_utils.get_format(call, field_name, vcf_object=reader)
self.assertEqual(actual, expected)
def test_get_format(self, field_name, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_get_fn.return_value = (
functools.partial(struct_utils.get_string_field,
is_single_field=True))
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, 'GP', [.1, .2, .7])
variantcall_utils.set_format(call, 'AD', [55, 3])
variantcall_utils.set_format(call, 'DP', 58)
variantcall_utils.set_format(call, 'GL', [-1, -3, -5.5])
variantcall_utils.set_format(call, 'GT', [0, 1])
variantcall_utils.set_format(call, 'FT', ['LowQual'])
actual = variantcall_utils.get_format(call,
field_name,
vcf_object=reader)
self.assertEqual(actual, expected)
def _get_vaf(variant, vcf_reader):
"""Gets the VAF (variant allele frequency)."""
vafs = variantcall_utils.get_format(
variant_utils.only_call(variant), 'VAF', vcf_reader)
return sum(vafs)