It sounds like you're trying to implement a one-time pad. Let me demonstrate with a couple of one-liners: 
thulben@bravo:~/perl
125> perl -le 'print "A" ^ "C"' | perl -nle 'print $_^"C"'
A
thulben@bravo:~/perl                                      
126> perl -le 'print "A" ^ "C"' | perl -nle 'print $_^"A"'
C
thulben@bravo:~/perl
127>

[download]
Basically, (X xor Y) xor X = Y for all X,Y. And, because the xor operation is equivalent to addition modulo 2 (or, as the algebraist might say "addition in the finite field with two elements"), this works. A canned solution? Here's a quicky: 
use warnings;
use strict;

my $cipher = shift;
my $key    = shift;

open( my $cipher_fh, $cipher ) or die $!;
open( my $key_fh,    $key )    or die $!;

my $buffer_length = 4_096;

while ( sysread( $cipher_fh, my $cipher_text, $buffer_length, )
     && sysread( $key_fh,    my $key_text,    $buffer_length, ) ) {

         print $cipher_text ^ $key_text;
}

[download]
I don't do a lot of error checking here, so there is room to improve.

thor

p.s. In case it wasn't obvious, you'll need to redirect the output from the script that I provided above: it prints to standard out

In reply to Re: Mod-2 add 2 binary files by thor
in thread Mod-2 add 2 binary files by tperdue

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