Just off the top of my head, I'd probably try replacing the 'pack' stuff by producing whole bytes at a time. Something like: 

use Algorithm::Loops qw< NestedLoops >;
my @bases= qw< A C G T >;
my @quad= map { join '', @$_ } NestedLoops( [ ( \@bases ) x 4 ] );
my %byte;
@byte{ @quad }= map pack("C",$_), 0 .. %#quad;

my $carry= '';
while( <> ) {
    chomp;
    substr( $_, 0, 0, $carry );
    my $pack= '';
    s/(....)/ $pack .= $byte{$1}; '' /g;
    $carry= $_;
    print RAM $pack;
}
print RAM $byte{ substr( $carry . 'AAA', 0, 4 ) }
    if  $carry;

[download]

But I haven't looked at the rest of this thread recently nor actually tried my suggestions. I can think of lots of different ways to pull out 4 bases at a time and some ways might have a noticeable impact on speed.

- tye        

In reply to Re^3: Sorting Gigabytes of Strings Without Storing Them (bytes) by tye
in thread Sorting Gigabytes of Strings Without Storing Them by neversaint

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