def test_is_variant_call_apply_filter(self, genotype, filters,
expected_when_applied,
expected_when_not_applied):
variant = test_utils.make_variant(gt=genotype, filters=filters)
# The default is apply_filter=True.
self.assertEqual(
variant_utils.is_variant_call(variant), expected_when_applied)
self.assertEqual(
variant_utils.is_variant_call(variant, apply_filter=True),
expected_when_applied)
self.assertEqual(
variant_utils.is_variant_call(variant, apply_filter=False),
expected_when_not_applied)
def test_is_variant_call(self, variant, expected_req_non_ref,
expected_any_genotype):
# Check that default call checks for genotypes.
self.assertEqual(
variant_utils.is_variant_call(variant), expected_req_non_ref)
# Ask explicitly for genotypes to be included.
self.assertEqual(
variant_utils.is_variant_call(variant, require_non_ref_genotype=True),
expected_req_non_ref)
# Don't require non_ref genotypes.
self.assertEqual(
variant_utils.is_variant_call(variant, require_non_ref_genotype=False),
expected_any_genotype)
with self.assertRaises(Exception):
variant_utils.is_variant_call(None)
def check_is_variant(variant, expected, **kwargs):
self.assertEqual(
variant_utils.is_variant_call(variant, **kwargs), expected)