Simplified GenomeFunction design by removing genome prototype and adding progress listener onto the GenomeReader instead. Finished Query abstract classes. Now implementing a GenomeReader that uses multiple threads to process queries in parallel.
implemented genome prereading to determine chromosome order and hashing this information so that preread only occurs once for each genome file. Working on the actual read behavior.
Created SequenceProvider class to handle synchronization of worker and reader threads. Working on implementing the worker threads
Working on implementing GenomeWorker still, initialization completed, working on processing logic. Added union method to GenomicRegion.