def get_count(bed):
    """
    Get number of lines in the bed file. If the chromosome,
    contains any of these substrings, then don't count
    """
    ignore_contigs = {'hs', 'GL', 'X', 'Y'}
    return len(set([line for line in open(bed).readlines()
                if all([ic not in line.split()[0] for ic in ignore_contigs])]))