Both Kmer and Seq (for Fastq) filter tools seems to be working.  I had to hack the seq output so that we use C output methods, rather than those that come with SeqAn.  The sequence filtering tool is tediously slow at the moment.  I should revisit this at some point to do some profiling and to see where it can be speeded up.  No doubt I am doing waaay too much string copying at the moment.