Made changes to <hmmgen_gene.pl>
Merge branch 'master' of https://github.com/KorfLab/Genesmith
Merge to add extra changes to <hmmgen_gene.pl>
Added the option to convert from a Standard gene model, with
3 CDS states, to a Basic gene model with 1 CDS state
- opt [-1] allow the conversion to Basic gene model
- opt [-S] removes Start and Stop states from Basic gene model

Scripts altered:
   - hmmgen_gene.pl
   - hmmgen_branch.pl
   - hmm_assmbl.pl