def test_wholly_contained_target() -> None:
target_inner = Interval("1", 50, 60)
target_outer = Interval("1", 40, 80)
run_test(targets=[target_inner, target_outer],
query=target_inner,
results=[target_outer, target_inner])
def test_multiple_references() -> None:
target_chr1 = Interval("1", 10, 20)
target_chr2 = Interval("2", 10, 20)
run_test(targets=[target_chr1, target_chr2],
query=target_chr1,
results=[target_chr1])
run_test(targets=[target_chr1, target_chr2],
query=target_chr2,
results=[target_chr2])
def test_get_enclosed() -> None:
a = Interval("1", 10, 100)
b = Interval("1", 15, 20)
c = Interval("1", 18, 19)
d = Interval("1", 50, 99)
detector = OverlapDetector()
detector.add_all([a, b, c, d])
assert detector.get_enclosed(Interval("1", 1, 250)) == [a, b, c, d]
assert detector.get_enclosed(Interval("1", 5, 30)) == [b, c]
assert detector.get_enclosed(Interval("1", 16, 20)) == [c]
assert detector.get_enclosed(Interval("1", 15, 19)) == [c]
assert detector.get_enclosed(Interval("1", 10, 99)) == [b, c, d]
def test_multiple_overlaps() -> None:
interval_a = Interval("1", 10, 20)
interval_b = Interval("1", 15, 25)
interval_c = Interval("1", 19, 30)
interval_d = Interval("1", 24, 35)
# B overlaps both A and C
run_test(targets=[interval_a, interval_c],
query=interval_b,
results=[interval_a, interval_c])
# C overlaps both A and B
run_test(targets=[interval_a, interval_b],
query=interval_c,
results=[interval_a, interval_b])
# D overlaps only B and C (is after A)
run_test(targets=[interval_a, interval_b, interval_c],
query=interval_d,
results=[interval_b, interval_c])
def test_same_interval_twice() -> None:
interval = Interval("1", 10, 100)
run_test(targets=[interval, interval], query=interval, results=[interval])
def test_different_references() -> None:
target = Interval("1", 10, 100)
query = Interval("2", 10, 100)
run_test(targets=[target], query=query, results=[])
def test_query_after_target() -> None:
target = Interval("1", 10, 100)
query = Interval("1", 100, 101)
run_test(targets=[target], query=query, results=[])
def test_query_before_target() -> None:
target = Interval("1", 10, 100)
query = Interval("1", 9, 10)
run_test(targets=[target], query=query, results=[])
def test_target_overlaps_last_base_of_query() -> None:
target = Interval("1", 10, 100)
query = Interval("1", 10, 11)
run_test(targets=[target], query=query, results=[target])
def test_target_wholly_contained_in_query() -> None:
target = Interval("1", 10, 100)
query = Interval("1", 9, 101)
run_test(targets=[target], query=query, results=[target])