#!/usr/bin/python3

"""
Find regions of first bed file that overlap regions in a second bed file. This
program performs a base-by-base intersection, so only runs of bases that are
covered in both of the inputs will be output.

usage: %prog bed_file_1 bed_file_2
"""

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

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

bits1 = binned_bitsets_from_file(open(in_fname))
bits2 = binned_bitsets_from_file(open(in2_fname))

bitsets = {}

for key in bits1:
    if key in bits2:
        bits1[key].iand(bits2[key])
        bitsets[key] = bits1[key]

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))