Remove non-increasing BED lines which will cause variant callers to choke.

    Also fixes space separated BED inputs.

def remove_bad():
    """Remove non-increasing BED lines which will cause variant callers to choke.

    Also fixes space separated BED inputs.
    """
    for line in sys.stdin:
        parts = line.strip().split("\t")
        if len(parts) == 1 and len(line.strip().split()) > 1:
            parts = line.strip().split()
        if line.strip() and len(parts) > 2 and int(parts[2]) > int(parts[1]):
            sys.stdout.write("\t".join(parts) + "\n")