def test_set_format(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_set_fn.return_value = (
struct_utils.set_string_field)
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, field_name, value, reader)
actual = call.info[field_name].values
self._assert_struct_lists_equal(actual, expected)
def test_set_format(self, field_name, value, reader, expected):
if reader is not None:
reader = mock.Mock()
reader.field_access_cache.format_field_set_fn.return_value = (
struct_utils.set_string_field)
call = variants_pb2.VariantCall()
variantcall_utils.set_format(call, field_name, value, reader)
actual = call.info[field_name].values
self._assert_struct_lists_equal(actual, expected)
def setUp(self):
super(VcfStatsTest, self).setUp()
self.variant = test_utils.make_variant(chrom='chr1',
start=10,
alleles=['A', 'G'],
gt=[0, 1],
gq=59)
variantcall_utils.set_format(variant_utils.only_call(self.variant),
'DP', 20)
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)