Add quick code for checking BCF files
Update javadoc for Plugin Feature interfaces
Add basic command line gatk_plugin

Still a long way from done, starting with UnifiedGenotyper
Add basic command line gatk_plugin

Still a long way from done, starting with UnifiedGenotyper
Update SamIndexerTest so it actually runs
Add method for creating BAM index to SamIndexer

Should probably reorganize this but we really just are calling through to Picard. Added unit test as well