Cgivar2vcf updates

Some (hopefully) trivial changes and cleanup:

  - `cgivar_to_vcf.py` wouldn't run unless I included 'twobit' from `get_reference.py` (instead of 'import .twobit')
  - Added some simple input checking for parameters passed to `cgvar_to_vcf.py` from the command line.
  - Updated the option parser.