#!/usr/bin/python3

"""
Find continuous regions that are covered by the first bed file (`bed_file_1`)
but not by the second bed file (`bed_file_2`)

usage: %prog bed_file_1 bed_file_2
"""

from bx.bitset_builders import binned_bitsets_from_file
from bx.cookbook import doc_optparse


def print_bits_as_bed(bits):
    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))


options, args = doc_optparse.parse(__doc__)
try:
    in_fname, in2_fname = args
except ValueError:
    doc_optparse.exit()

# Read first bed into some bitsets

bitsets1 = binned_bitsets_from_file(open(in_fname))
bitsets2 = binned_bitsets_from_file(open(in2_fname))

for chrom in bitsets1:
    if chrom not in bitsets1:
        continue
    bits1 = bitsets1[chrom]
    if chrom in bitsets2:
        bits2 = bitsets2[chrom]
        bits2.invert()
        bits1.iand(bits2)
    print_bits_as_bed(bits1)