Updates to indel realigner to improve performance and accuracy.
Remove extraneous implicit methods
Merge pull request #314 from fnothaft/indel-realigner-rebase

Updates to indel realigner to improve performance and accuracy.
Merge pull request #320 from genomebridge/remove-implicit-methods

Remove extraneous implicit methods in ReferenceMappingContext
Adding code for lifting over between sequences and the reference genome.
Merge pull request #306 from fnothaft/liftover

Adding code for lifting over between sequences and the reference genome.
[REMOVE ME] A missing 'index' argument to the Features2ADAM CLI was causing an error when running that command.

Simplifying two map arguments, where we don't need the '_'
Stub Gene, Transcript, Exon classes.