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) A VcfReader or VcfWriter object. 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)