#!/usr/bin/perl -w
use strict;
use warnings;
use Data::Dump qw/dump/;

my %data;

foreach my $filename (qw/one.txt two.txt three.txt/) {
    open( my $file, $filename )
        or die "Unable to open $filename because $!\n";
    while (<$file>) {
        chomp;
        my ( $chrX, $chrpos, $value1, $value2 ) = split(/\s+/);
        $data{$chrX}->{$chrpos}->{'value1'} += $value1;
        $data{$chrX}->{$chrpos}->{'value2'} += $value2;
    } ## end while (<$file>)
} ## end foreach my $filename (qw/one.txt two.txt three.txt/)

print dump( \%data );

##</code><code>##

one.txt
chromosome1 50000 12 20
chromosome2 20000 0 21
chromosome3 41444 9 2
chromosome4 21414 4 1 
.
.
.
(there would be 5million lines of the above)