#your code
#my $infile = $ARGV[0];  
#my $infile2 = $ARGV[0];  <--- $infile == $infile2
#corrected code
my $infile = $ARGV[0];
my $infile2 = $ARGV[1];


##</code><code>##

#yourcode
while (<INFILE>){
    chomp;
    my @line = split ('\t', $_);
    my $key1 = 'A' . $line[0] . '.' . 'A' . $line[1]; ##first key
    my $key2 = 'A' . $line[1] . '.' . 'A' . $line[0]; ##key the other 
+way
    ##check to see if the key exists in the hash
     ##if it doesn't there is data in your infile, not in you names ar
+ray
    if (exists $diplotypes{$key1} && $line[0] <= $line[1]) {
        $diplotypes{$key1} += $line[2];
        }
    elsif (exists $diplotypes{$key2} && $line[0] >= $line[1]) {
        $diplotypes{$key2} += $line[2];
        }
    else{##world is out to get you
        print STDERR "No key for $key1 or $key2\n";
        next;
    }
}


##</code><code>##

while (<INFILE>){
    chomp;
    my @line = split ('\t', $_);
    my $key1 = 'A' . $line[0] . '.' . 'A' . $line[1]; ##first key
    my $key2 = 'A' . $line[1] . '.' . 'A' . $line[0]; ##key the other way
    ##check to see if the key exists in the hash
    ##if it doesn't there is data in your infile, not in you names array
	##new logic
	if($line[0] <= $line[1]) {
		if(exists $diplotypes{$key1}) {
			$diplotypes{$key1} += $line[2];
		}
		else { 
			#key doesnt exist so add it
			$diplotypes{$key1} = $line[2];
		}
	}
	else {
		if(exists $diplotypes{$key2}) {
			$diplotypes{$key2} += $line[2];
		}
		else { 
			#key doesnt exist so add it
			$diplotypes{$key2} = $line[2];
		}
	}
}}