#!/usr/bin/perl -w
use strict;
use POSIX qw/ceil/;	

use Data::Dumper;

my %bases = ('a'=>[0,0], 'c'=>[0,1], 'g'=>[1,0], 't'=>[1,1]);
my %bvals = ('00'=>'a', '01'=>'c','10'=>'g','11'=>'t');

my $DNA = 'acgtagattaatcgagctagcctgatgcgatcgatcgagagggtctctttattctgatcgatcgcgctagatagcgatcgatcgatcgatacacagttataacagagtcttatatca';

my $DNA_frag1 = 'gatc';
my $DNA_frag2 = 'gcct';

sub DNA_pack
{
	my $instr = shift;
	my $vt = 0 x ceil(length($instr)/4);
	my $mo = length($instr) * 2;
	my @c = split(//,$instr);
	my $bi = 0;
	while(my $c = shift(@c)){
		my @b = @{$bases{$c}};
		vec($vt, $bi, 1) = shift @b;
		vec($vt, $bi+1, 1) = shift @b;
		$bi += 2;
	}
	return [$mo,$vt];
}

sub DNA_unpack
{
	return join('',(map{m/\d\d/?$bvals{$_}:()}split(/(\d\d)/,unpack("b$_[0]->[0]",$_[0]->[1]))));
}