vcfnulldotslashdot

#!/usr/bin/env python3
# Rewrite null genotypes to ./.
#
import sys
import math

def bincoeff(n,k): return math.factorial(n) / (math.factorial(n-k)*math.factorial(k))
def multcoeff(n,k): return bincoeff(n+k-1,k)

if len(sys.argv) > 1:
    inf = open(sys.argv[1])
else:
    inf = sys.stdin

for line in inf:
    if line.startswith("#"):
        print(line.strip())
        continue
    fields = line.strip().split("\t")
    alleles = len(fields[4].split(","))+1
    # assume that we have GT:GL
    # how many genotypes?  assume diploid
    flatgls = ",".join([str(x) for x in [0]*int(multcoeff(alleles,2))])
    for i in range(9, len(fields)):
        if fields[i] == ".":
            fields[i] = "./.:" + flatgls
    print("\t".join(fields))