def test_variants_overlap(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=20)
with mock.patch.object(ranges, 'ranges_overlap') as mock_overlap:
mock_overlap.return_value = 'SENTINEL'
self.assertEqual(variant_utils.variants_overlap(v1, v2), 'SENTINEL')
mock_overlap.assert_called_once_with(
variant_utils.variant_range(v1), variant_utils.variant_range(v2))
def test_variants_overlap(self):
v1 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=10)
v2 = test_utils.make_variant(chrom='1', alleles=['A', 'C'], start=20)
with mock.patch.object(ranges, 'ranges_overlap') as mock_overlap:
mock_overlap.return_value = 'SENTINEL'
self.assertEqual(variant_utils.variants_overlap(v1, v2), 'SENTINEL')
mock_overlap.assert_called_once_with(
variant_utils.variant_range(v1), variant_utils.variant_range(v2))
def split_independent_variants(variants_and_genotypes):
"""Splits variants_and_genotypes into an overlapping group and remaining."""
if not variants_and_genotypes:
raise ValueError('Expected at least one value in variants_and_genotypes')
overlaps = [variants_and_genotypes[0]]
for i in range(1, len(variants_and_genotypes)):
vgi = variants_and_genotypes[i].variant
if any(variant_utils.variants_overlap(vg.variant, vgi) for vg in overlaps):
overlaps.append(variants_and_genotypes[i])
else:
return overlaps, variants_and_genotypes[i:]
return overlaps, []
def split_independent_variants(variants_and_genotypes):
"""Splits variants_and_genotypes into an overlapping group and remaining."""
if not variants_and_genotypes:
raise ValueError('Expected at least one value in variants_and_genotypes')
overlaps = [variants_and_genotypes[0]]
for i in range(1, len(variants_and_genotypes)):
vgi = variants_and_genotypes[i].variant
if any(variant_utils.variants_overlap(vg.variant, vgi) for vg in overlaps):
overlaps.append(variants_and_genotypes[i])
else:
return overlaps, variants_and_genotypes[i:]
return overlaps, []
