Starting to refactor REDHAWK_eval.  Following changes so far:
1) Removed the "organize" option to make organization automatic.
   -- There will now be seperate output directories for each phase.
2) Added parameters to control resulting directury stucture.
3) Began to refactor code to consolidate calls to RAIDER and such.
4) Minor changes to various functions to accomodate above changes.

Code is tested up through the call to the simulator.  Original code
remains, but has been commented out.
Working on refactored RAIDER call.  (Not finished.)
Continuing refactoring: now runs RAIDER.  (Only tested for simulated chromosomes.)
Extended refactoring to raider consensus sequence building.  Appears to be working.  However, it appears there might be a bug in the consensus sequence software.
Fixed consensus_seq.py; now requires 2 output file names.  (One for the coordinate description, and one for the .fa description.)