loop(0);


# the next section takes each route and counts the number of unique snp's for each route

# for the num of possible routes through the matrix
for $i (0 ... $#finalroute)
{
    $number_of_unique_columns=0;
    %count=();

    
# for each step of the particular route we are looking at
    for (@{$finalroute[$i]}) 
    {
	$count{$_}++;        
    }  
# this loop counts the number of keys , therefore gives the number of columns used in this route thru the matrix                      
    for (keys %count)         
    {
	$number_of_unique_columns++;                        
    }
    $route[$i]=$number_of_unique_columns;
}

#  $column_limit is user input set at the beginning and is the cut-off for the num of columns used                                        
for $i ( 1 ... $column_limit )
{

#step the route array which has the number of columns used #for each route. If it equals the $i value (number of #columns) we
#are currently looking at then print out the route thru the #matrix that is associated with it i.e @{$finalroute[$_]}
    for (0 ... $#route)           
    {                    
	print "@{$finalroute[$_]}\n$route[$_]\n" if  $route[$_]==$i;
    }
}






sub loop{


    my ($row,@array)=@_  ;
    
    
    for (1 ... $#number_of_columns)
    {
	push @array,$_ if $matrix[$row][$_] ==1;
	
	my $length=@array;
	my $lengthofmatrix=@matrix;

	if ($row==$lengthofmatrix)
       {
	       $finalroute[$block][$y]=[@array] if                        $length==$lengthofmatrix;
	       $y++ if $length==$lengthofmatrix;      
	}
	else
	{
	    loop($row+1,$block,@array);
	}
	
	pop @array if $matrix[$row][$_]==1;
	
    }

        
}