Adding support for partial genes

Shortly:
* prodigal can now be run without the -c option
* prodigal's gff output is now parsed with Bio::Tools:GFF, using the 'partial' tag of prodigal to find gene running off edges.
* Bio::Location::Fuzzy is used to correctly set start and end of CDSs. I also set the frame and codon_start attributes.
* Some tweaking is performed to correctly print the tbl file, but I think I covered all possible cases.
* Added a new --partialgenes option to prokka