def get_variant_ad(variant):
"""Returns the allele depth for the Variant, calculated across its calls."""
num_alleles = len(variant.alternate_bases) + 1
call_ads = [variantcall_utils.get_format(vc, 'AD') for vc in
variant.calls]
assert(len(call_ad) == num_alleles for call_ad in call_ads)
return [sum(call_ad[i] for call_ad in call_ads) for i in xrange(num_alleles)]
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)