You probably want to read each file explicitly and use a "last" (or a breaking variable) to exit the loop when done. something like:
my $more_to_read = 1;
while($more_to_read){
$more_to_read = 0 if(eof(F1) && eof(F2));
my $f1 = <F1>;
my $f2 = <F2>;
#some processing here
}
UPDATE: You should probably use strict and warnings, it will give you better diagnostic info on what actually went wrong
They say that time changes things, but you actually have to change them yourself. —Andy Warhol
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