Some new features with stable code base

The instability of the most recent release v0.0.7 resulted in reverting back to the v0.0.3 code base and adding some of the new features in a more robust way. The major changes in this beta release are the additional functional modes that can be executed (run, start_blat_server, prepare_reference_data). There are a handful of major and minor bug fixes and much of the code has been refactored and organized into proper modules for future development. The output files have been simplified into a single output file containing the most relevant information.

More testing and a few more minor changes will take place before this becomes a full release.