#!/usr/bin/env python

import sys,os.path

f = open(os.path.splitext(sys.argv[1])[0] + ".avinput", "w+")

for line in open(sys.argv[1]):
	if line[0] == "#": continue
	fields = line.rstrip().split("\t")
	#sys.stderr.write(str(fields) + "\n")
	alts = fields[4].split(",")
	alt = ""
	gt = fields[9].split(":")[0]
	if "1" in gt.split("/"):
		alt = alts[0]
	elif "2" in gt.split("/"):
		if alts[1:]:
			alt = alts[1]
		else:
			alt = alts[0]
	elif "3" in gt.split("/"):
		if alts[2:]:
			alt=alts[2]	
		else:
			alt= alts[0]
	else:
		alt = alts[0]
	f.write("\t".join([fields[0],fields[1],str(int(fields[1]) + len(fields[3])-1),fields[3],alt,"GT:" + gt]) + "\n")