def test_prune_alleles_handles_format_fields(self, alts, to_remove, orig_ad,
expected_ad):
variant = _create_variant_with_alleles(alts=alts)
test_utils.set_list_values(variant.calls[0].info['AD'], orig_ad)
actual = postprocess_variants.prune_alleles(variant, to_remove)
self.assertEqual([v.int_value for v in actual.calls[0].info['AD'].values],
expected_ad)
def test_prune_alleles_handles_format_fields(self, alts, to_remove, orig_ad,
expected_ad):
variant = _create_variant_with_alleles(alts=alts)
test_utils.set_list_values(variant.calls[0].info['AD'], orig_ad)
actual = postprocess_variants.prune_alleles(variant, to_remove)
self.assertEqual([v.int_value for v in actual.calls[0].info['AD'].values],
expected_ad)
def test_simplify_alleles(self, alleles, alt_alleles_to_remove, expected):
"""Test that prune_alleles + simplify_alleles works as expected."""
variant = _create_variant_with_alleles(ref=alleles[0],
alts=alleles[1:])
pruned = postprocess_variants.prune_alleles(variant,
alt_alleles_to_remove)
simplified = postprocess_variants.simplify_alleles(pruned)
self.assertEqual(simplified.reference_bases, expected[0])
self.assertEqual(simplified.alternate_bases, expected[1:])
def test_simplify_alleles(self, alleles, start, alt_alleles_to_remove,
expected_alleles, expected_end):
"""Test that prune_alleles + simplify_alleles works as expected."""
variant = _create_variant_with_alleles(
ref=alleles[0], alts=alleles[1:], start=start)
pruned = postprocess_variants.prune_alleles(variant, alt_alleles_to_remove)
simplified = postprocess_variants.simplify_alleles(pruned)
self.assertEqual(simplified.reference_bases, expected_alleles[0])
self.assertEqual(simplified.alternate_bases, expected_alleles[1:])
self.assertEqual(simplified.start, start)
self.assertEqual(simplified.end, expected_end)
def test_prune_alleles(self, canonical_variant, alt_alleles_to_remove,
expected_variant):
self.assertEqual(
postprocess_variants.prune_alleles(
canonical_variant, alt_alleles_to_remove), expected_variant)
def test_prune_alleles(self, canonical_variant, alt_alleles_to_remove,
expected_variant):
self.assertEqual(
postprocess_variants.prune_alleles(
canonical_variant, alt_alleles_to_remove), expected_variant)