>  while ($i < $num) {
>     $sortedKeys[$i] = $i;
>     $i++;
>  }

##</code><code>##

@sortedKeys = (0 .. $num - 1);

##</code><code>##

>  next unless defined %{$matches{$fasta_id}};
>  last unless defined @{$matches{$fasta_id}{$site}};

##</code><code>##

>  # as @fastarray is global, this will have global effect, and we do not need to return it.
>
>  @fastarray=@newfast;