[12:47:29.37] c:\test>junk4 ACGT34.dat >nul
[12:50:49.45] c:\test>

[12:53:00.73] c:\test>sort ACGT34.dat /O nul
[12:53:09.51] c:\test>

##</code><code>##

#!/usr/bin/perl
use strict;
use warnings;

use Sort::Packed qw(sort_packed);

my $packed = '';
open RAM, '>', \$packed;
seek RAM, 10e6, 0;
print RAM chr(0);
seek RAM, 0, 0;

my ($len);

my %val = (A => 0, C => 1, G => 2, T => 3);
my %rev = reverse %val;

sub compress {
    my @data = split //, scalar(reverse shift);
    my $out = '';
    for (my $i = 0; $i < @data; $i++) {
        my $bits = $val{$data[$i]};
        defined $bits or die "bad data";
        vec($out, $i, 2) = $bits;
    }
    scalar reverse $out
}

sub decompress {
    my $data = reverse shift;
    my $len = shift;
    my $out;
    for (my $i = 0; $i< $len; $i++) {
        $out .= $rev{vec($data, $i, 2)}
    }
    scalar reverse $out;
}

while(<>) {
    chomp;
    ($len ||= length) == length or die "bad data";
    print RAM compress $_;
}
close RAM;
chop $packed while length( $packed ) > $. *9;

my $bytes = int(($len * 2 + 7) / 8);
my $n = length($packed) / $bytes;

sort_packed "C$bytes" => $packed;

for (my $i = 0; $i < $n; $i++) {
    print decompress(substr($packed, $i * $bytes, $bytes), $len), "\n";
}
__END__
[13:50:49.29] c:\test>junk4 ACGT34.dat >nul

[13:53:44.53] c:\test>