[ADAM-327] Adding gene, transcript, and exon models.

A few major changes in these commits: 

* Upgrading to bdg-formats 0.3.1
* This version of bdg-formats changes the Pileup schema, so we fix all the errors that this introduces -- and we _eliminate_ the Pileup aggregation code
* This version of bdg-formats also changes the Feature schema, so we've updated the feature parsing code to create these new features correctly
* The FeatureHierarchy classes have been rewritten as wrappers around Feature
* Added Gene, Transcript, Exon, and UTR case classes to represent gene models, and added code for assembling them from 'flat' Features.




I have no idea.  But basically, if you put this import at the top level, then all the implicit conversions from java.util.List to the Scala equivalents (basically, all the JavaConversions) blow up in the Gene transformation code below.