#!/usr/bin/env python
##coding=utf-8

import os
import sys
import argparse
import vcf

parser = argparse.ArgumentParser(description="")
parser.add_argument('-i', '--invcf', help = 'the input vcf file', required = True)
parser.add_argument('-o', '--outvcf', help = 'the output vcf file', required = True)
argv = vars(parser.parse_args())
inF = os.path.abspath(argv['invcf'].strip())
ouF = os.path.abspath(argv['outvcf'].strip())

def parser_vcf(infile,outfile):
    samplename=str(str(str(infile).strip().split('/')[-1]).strip().split("_")[0])
    vcf_r=vcf.Reader(filename=infile)
    for record in vcf_r:
        if len(record.FILTER) == 0 :
            print("samplename: "+str(samplename))
            sample1=samplename+".Mutect2"
            sample2=samplename+".vardict"
            print("sample1: "+str(record.genotype(sample1)['GT']))
            break
#            if record.samples[sample2]['DP'] == "." and record.samples[sample2]['GT'] == ".":

parser_vcf(inF,ouF)