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#!/usr/bin/python3
"""
Merge any overlapping regions of bed files. Bed files can be provided on the
command line or on stdin. Merged regions are always reported on the '+'
strand, and any fields beyond chrom/start/stop are lost.
usage: %prog bed files ...
"""
import fileinput
import sys
from bx.bitset_builders import binned_bitsets_from_bed_file
bed_filenames = sys.argv[1:]
if bed_filenames:
input = fileinput.input(bed_filenames)
else:
input = sys.stdin
bitsets = binned_bitsets_from_bed_file(input)
for chrom in bitsets:
bits = bitsets[chrom]
end = 0
while True:
start = bits.next_set(end)
if start == bits.size:
break
end = bits.next_clear(start)
print("%s\t%d\t%d" % (chrom, start, end))
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