def test_query_overlaps_interval_start():
lapper = setup_nonoverlapping()
cursor = Cursor(0)
expected = Interval(20, 30, 0)
assert expected == next(lapper.find(15, 25))
assert expected == next(lapper.seek(15, 25, cursor))
assert list(lapper.find(15, 25)) == list(lapper.seek(15, 25, Cursor(0)))
def test_query_overlaps_interval_stop():
"""Test that a query that overlaps the stop of an interval returns that interval"""
lapper = setup_nonoverlapping()
cursor = Cursor(0)
expected = Interval(20, 30, 0)
assert expected == next(lapper.find(25, 35))
assert expected == next(lapper.seek(25, 35, cursor))
assert list(lapper.find(25, 35)) == list(lapper.seek(25, 35, Cursor(0)))
def test_overlapping_intervals():
"""Test interval overlaps are working properly"""
lapper = setup_overlapping()
cursor = Cursor(0)
e1 = Interval(0, 15, 0)
e2 = Interval(10, 25, 0)
assert [e1, e2] == list(lapper.find(8, 20))
assert [e1, e2] == list(lapper.seek(8, 20, cursor))
assert list(lapper.find(8, 20)) == list(lapper.seek(8, 20, Cursor(0)))
def test_query_envelops_interval():
"""Test that a query that envolops an interval returns that interval"""
lapper = setup_nonoverlapping()
cursor = Cursor(0)
expected = Interval(20, 30, 0)
assert expected == next(lapper.find(15, 35))
assert expected == next(lapper.seek(15, 35, cursor))
assert list(lapper.find(15, 35)) == list(lapper.seek(15, 35, Cursor(0)))
def test_interval_envelops_query():
"""Test that a query that is enveloped by interval returns interval"""
lapper = setup_nonoverlapping()
cursor = Cursor(0)
expected = Interval(20, 30, 0)
assert expected == next(lapper.find(22, 27))
assert expected == next(lapper.seek(22, 27, cursor))
assert list(lapper.find(22, 27)) == list(lapper.seek(22, 27, Cursor(0)))
def test_query_start_interval_stop():
lapper = setup_nonoverlapping()
cursor = Cursor(0)
with pytest.raises(StopIteration):
next(lapper.find(30, 35))
with pytest.raises(StopIteration):
next(lapper.seek(30, 35, cursor))
def test_find_over_behind_first_match():
"""Test that if lower_bound puts us before the first match, we still return a match"""
lapper = setup_bad_lapper()
e1 = Interval(50, 55, 0)
found = next(lapper.find(50, 55))
assert found == e1
assert list(lapper.find(50, 55)) == list(lapper.seek(50, 55, Cursor(0)))
def test_seek_over_overlapping():
"""Test that seeking for all intervals over self == len(self)"""
lapper = setup_overlapping()
cursor = Cursor(0)
total = 0
for iv in lapper:
for fiv in lapper.seek(iv.start, iv.stop, cursor):
total += 1
assert total == 28
def test_seek_over_len():
"""Test that it's not possible to induce index out of bounds by pushing the cursor past the end of the lapper."""
lapper = setup_nonoverlapping()
single = setup_single()
cursor = Cursor(0)
for interval in lapper.intervals:
for o_interval in single.seek(interval.start, interval.stop, cursor):
print(o_interval)
def main():
ivs = make_random(200_000, 50_000_000, 3)
ivs_sorted = sorted(ivs, key=lambda x: x.start)
lapper = Lapper(ivs)
print("Lapper find:")
total = 0
for iv in ivs:
found = sum(1 for f in lapper.find(iv.start, iv.stop))
total += found
print(total)
print("Lapper seek")
total = 0
cursor = Cursor(0)
for iv in lapper.intervals:
total += sum(1 for f in lapper.seek(iv.start, iv.stop, cursor))
print(total)
def test_bad_skips():
"""When there is a very long interval that spans many little intervals, test that the little intevals still get returne properly"""
data = [
Interval(25264912, 25264986, 0),
Interval(27273024, 27273065, 0),
Interval(27440273, 27440318, 0),
Interval(27488033, 27488125, 0),
Interval(27938410, 27938470, 0),
Interval(27959118, 27959171, 0),
Interval(28866309, 33141404, 0),
]
lapper = Lapper(data)
found = list(lapper.find(28974798, 33141355))
assert found == [Interval(28866309, 33141404, 0)]
assert list(lapper.find(28974798, 33141355)) == list(
lapper.seek(28974798, 33141355, Cursor(0)))
def test_seek_over_short_stop():
"""Test that seek is not stopping early"""
lapper = Lapper([
Interval(0, 1, 0),
Interval(0, 1, 0),
Interval(1, 2, 0),
])
cursor = Cursor(0)
seek_total = 0
for iv in lapper:
for fiv in lapper.seek(iv.start, iv.stop, cursor):
seek_total += 1
find_total = 0
for iv in lapper:
for fiv in lapper.find(iv.start, iv.stop):
find_total += 1
assert seek_total == 5
assert find_total == 5
from py_lapper import Interval, Lapper, Cursor intervals = [Interval(0, 5, True), Interval(4, 8, True), Interval(9, 12, True)] lapper = Lapper(intervals) found = [iv for iv in lapper.find(4, 7)] # found = [Interval(0, 5, True), Interval(4, 8, True)] # Use seek when you will have many queries in sorted order. cursor = Cursor(0) found = [iv for iv in lapper.seek(1, 4, cursor)] # found = [Interval(0, 5, True)] # cursor = Cursor(2) found = [iv for iv in lapper.seek(5, 7, cursor)] # found = [Interval(4, 8, True)] # cursor = Cursor(3)