Only make a gene catalog

[jgolob]

Allow users to use geneshot to only make a gene catalog and not proceed with any annotation / CAG steps thereafter.

Useful for alternative analyses (i.e. a known set of homologs to target; allelic varation of a single gene like PBP2, etc).

[adriaaula]

it would be cool to have also only the last part: calculate CAGs from a dataset of interest. Many people (me) will reach this software after having already the whole gene catalog built :)

[sminot]

That's a great point, @adriaaula! I'd be more than happy to review and merge in any additional functionality that you (or anyone else) would like to contribute.