#declare all filenames
$filename1 = 'one.txt';
$filename2 = 'two.txt';
$filename3 = 'three.txt';

##</code><code>##

#open text file 1

open (FILE1, $filename1) or die "Unable to open $filename1 because $!\n";

##</code><code>##

# Store the contents of the first file into $hash{col1_col2}

open (FILE1, $filename1) or die "Unable to open $filename1 because $!\n";
while ($line = <FILE1>) {
    chomp ($line);
    ($chrX, $chrpos, $value1, $value2) = split (/\t/, $line);
    $key1 = join ("_", $chrX, $chrpos);
    $hash{$key1}++;
};
close FILE1;

##</code><code>##

while ($line = <FILE2>) {
    chomp ($line);
    ($chrX, $chrpos, $value11, $value22) = split (/\t/, $line);
    $key2 = join ("_", $chrX, $chrpos);
if (exists $hash{$key2} > 0) {
    $hash{key2} = $value11 + $value1;
    $hash{key2} = $value22 + $value2;
    $hash{key2}++
}
};

##</code><code>##

while ($line = <FILE2>) {
    chomp ($line);
    ($chrX, $chrpos, $value11, $value22) = split (/\t/, $line);
    $key2 = join ("_", $chrX, $chrpos);
    if (exists $hash{$key2} > 0) {
        $hash{key2} = $value11 + $value1;
        $hash{key2} = $value22 + $value2;
        $hash{key2}++
    }
};

##</code><code>##

open (FILE2, $filename2) or die "Unable to open $filename2 because $!\n";

while ($line = <FILE2>) {
    chomp ($line);
    ($chrX, $chrpos, $value11, $value22) = split (/\t/, $line);
    $key2 = join ("_", $chrX, $chrpos);
if (exists $hash{$key2} > 0) {
    $hash{key2} = $value11 + $value1;
    $hash{key2} = $value22 + $value2;
    $hash{key2}++
}
};
close FILE2;

##</code><code>##

sub process_file {
    my $filename = shift or die "Missing filename!";
    open (FILE, $filename) or die "Unable to open $filename because $!\n";

    while ($line = <FILE2>) {
        chomp ($line);
        ($chrX, $chrpos, $value11, $value22) = split (/\t/, $line);
        $key2 = join ("_", $chrX, $chrpos);
        if (exists $hash{$key2} > 0) {
            $hash{key2} = $value11 + $value1;
            $hash{key2} = $value22 + $value2;
            $hash{key2}++
        }
    }
    close FILE;
}

##</code><code>##

process_file($filename2);
process_file($filename3);