#!/usr/bin/perl -w

use warnings;
use strict;
use autodie;

        # revise CHROM, POS and ID in the file(vcf) from stacks 
              
        open stacks, "batch_1.vcf" or die;   # the file is the output file in the pipeline "populations";
        
        
        open OUT, ">3pine_stacks.vcf" or die;
        
     
        
        
   while (<stacks>){
        	
                
        	chomp;
        	if(/^#/){
        		print OUT $_;
        	}else{
                my $i=0; 
		my @temp=split /\t/,$_;
        	$temp[0]=$temp[2];
        	$temp[1]=$temp[1]-(($temp[2]-1)*80);
        	$temp[2]=".";
        	for($i=0;$i<=$#temp;$i++){
        	print OUT $temp[$i]."\t";
   }
                 
                }
                print OUT "\n";
   }
close stacks;