#!/usr/bin/python
import IO
import sys
import getopt
import os

def main(argv):
    infile, outfile = '', ''
    var_dir = "/Net/mus/data/www/19genomes/variants.tables/"
    try:
        opts, args = getopt.getopt(argv,"hi:o:v:",["ifile=","ofile=","varfile="])
    except getopt.GetoptError:
        print 'test.py -i <inputfile> -o <outputfile>'
        sys.exit(2)
    for opt, arg in opts:
        if opt == '-h':
            print 'run: python filter.variant.calls.py -i infile -o outfile [-v varfile]'
            sys.exit(2)
        if opt == '-i':
            infile = arg
        if opt == '-o':
            outfile = arg
        if opt == '-v':
            vardir == arg
    sdi_only_variants(vardir, infile, outfile)