def test_overlap_crosstest(self):
count, min_start, max_start, max_len = 250, 1, 10000, 20
step_size = 25
ivs = self.create_intervals(count, min_start, max_start, max_len)
loop_iv_start = min_start - step_size - 1
tree = IVTree()
for iv in ivs:
tree.insert(iv)
for i in range(loop_iv_start, max_start, step_size):
test_iv = GenomicInterval(i, i + step_size)
naive_ovl_count = 0
for iv in ivs:
if test_iv.overlaps(iv):
naive_ovl_count += 1
ovl_all = list(tree.query_all_overlaps(test_iv))
ovl_all_count = len(ovl_all)
self.assertEqual(ovl_all_count, naive_ovl_count)
ovl_iv = tree.query_overlap(test_iv)
ovl = tree.has_overlap(test_iv)
if ovl_all_count > 0:
self.assertIsNotNone(ovl_iv)
self.assertTrue(ovl)
else:
self.assertIsNone(ovl_iv)
self.assertFalse(ovl)
def test_iv_overlap(self):
iv1 = GenomicInterval(1, 3)
iv2 = GenomicInterval(4, 5)
iv3 = GenomicInterval(5, 6)
iv4 = GenomicInterval(1, 2)
iv5 = GenomicInterval(1, 1)
iv6 = GenomicInterval(3, 3)
self.assertFalse(iv1.overlaps(iv2))
self.assertTrue(iv2.overlaps(iv3))
self.assertFalse(iv4.overlaps(iv2))
self.assertTrue(iv2.overlaps(iv3))
self.assertTrue(iv5.overlaps(iv1))
self.assertTrue(iv6.overlaps(iv1))