1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
|
"""
High level operations on genomic intervals. Most accept and produce iterables
of `bx.io.inervals.io.GenomicInterval` objects.
"""
BED_DEFAULT_COLS = 0, 1, 2, 5
MAX_END = 512 * 1024 * 1024
def bits_set_in_range(bits, range_start, range_end):
"""
Yield start,end tuples for each span of set bits in [range_start,range_end)
"""
end = range_start
while True:
start = bits.next_set(end)
end = min(bits.next_clear(start), range_end)
if start >= end:
break
yield start, end
def bits_clear_in_range(bits, range_start, range_end):
"""
Yield start,end tuples for each span of clear bits in [range_start,range_end)
"""
end = range_start
while True:
start = bits.next_clear(end)
if start >= range_end:
break
end = min(bits.next_set(start), range_end)
yield start, end
|
