#! /usr/bin/perl -w

use 5.010;

open (REF, "ref_snp.txt");
open (GENOTYPE, "$ARGV[0]");
open (OUT, ">$ARGV[1]");


my %genotype;
my %ref;
while(<GENOTYPE>) 

{
if (/(\d+)\t\w\t(\w)/) 
{
%genotype=($1=>$2,);
my @position=keys %genotype;
   #foreach $position (sort keys %genotype) 
   # {
   
# print OUT "$position\t$genotype{$position}\n";   
   # }
}
else 
{
print "It doesn'y match!$_ not match!\n\n";
}
   

}

while (<REF>)
{
if (/(\d+)\t(\w)/)
{
%ref = ($1=>$2,);
my @position_ref = keys %ref;
foreach $position_ref (sort keys %ref)
{
if (exists $genotype{$position_ref}) 
{
print OUT "$position_ref\t$genotype{$position_ref}\n";
}
else 
{
$genotype{$position_ref}=$ref{$position_ref};
print OUT "$position_ref\t$genotype{$position_ref}\n";
}
}
}

}