contig and singlet to fasta works now
added framework for calculating mismatches in contig
implemented contig_mismatches() and returns to run_tests()
commented out ace output functionality as Bio::Assembly::IO::ace writes wrong coordinates for reads/BACs in the contig
added functionality to write out contig and singleton fasta files to out dir. Not using mismatch as Bio::Seq objects not created properly in contig_mismatch() for test ACE file. Works fine for hand created ACE object.
cleaned up dox
writing fasta in all uppercase.