[ADAM-381] Fixes Pileup usage in bdg-formats 0.3.1

Removing the usage of now-deleted fields in the new Pileup schema.
[ADAM-327] Adding Gene, Transcript, and Exon models
Testing and test files.
[TO BE REMOVED] BIG test files.
Added the Alphabet trait and DNAAlphabet implementation.

Updated BlockExtractable to take an Alphabet parameter, and to use the DNAAlphabet by default.
Removing the Gene object, per Uri's suggestion.
Removed Extractable trait on Transcript, and replaced the method with three different methods (again, per Uri's suggestion) for extracting transcript-related sequences.
Rewriting the parsers and FeatureHierarchy using new Feature schema.
Cleaning up tests.
Fixing the CLI commands