def test_reserved_info_field_get_fn(self):
info = variants_pb2.Variant().info
values = ['C']
struct_utils.set_string_field(info, 'AA', values)
get_fn = vcf_constants.reserved_info_field_get_fn('AA')
actual = get_fn(info, 'AA')
self.assertEqual(actual, values[0])
def test_reserved_info_field_get_fn(self):
info = variants_pb2.Variant().info
values = ['C']
struct_utils.set_string_field(info, 'AA', values)
get_fn = vcf_constants.reserved_info_field_get_fn('AA')
actual = get_fn(info, 'AA')
self.assertEqual(actual, values[0])
def get_info(variant, field_name, vcf_object=None):
"""Returns the value of the `field_name` INFO field.
The `vcf_object` is used to determine the type of the resulting value. If it
is a single value or a Flag, that single value will be returned. Otherwise,
the list of values is returned.
Args:
variant: Variant proto. The Variant of interest.
field_name: str. The name of the field to retrieve values from.
vcf_object: (Optional) nucleus.io.vcf.Vcf{Reader,Writer}. If not None, the
type of the field is inferred from the associated VcfReader or VcfWriter
based on its name. Otherwise, the type is inferred if it is a reserved
field.
"""
if vcf_object is None:
get_field_fn = vcf_constants.reserved_info_field_get_fn(field_name)
else:
get_field_fn = vcf_object.field_access_cache.info_field_get_fn(field_name)
return get_field_fn(variant.info, field_name)
def test_invalid_reserved_info_field_get_fn(self, field):
with self.assertRaisesRegexp(ValueError,
'Unknown reserved INFO field to get:'):
vcf_constants.reserved_info_field_get_fn(field)
def test_invalid_reserved_info_field_get_fn(self, field):
with self.assertRaisesRegexp(ValueError,
'Unknown reserved INFO field to get:'):
vcf_constants.reserved_info_field_get_fn(field)
