(1) Confirmed that the merging of old and new DupHMM methods was successful, at least for mode 1. Mode 2 is still taking a while to complete at time of commit. DupHMM.py (which contained only k-means clustering algorithm) has been deleted, while OldDupHMM.py (containing the merging of both methods into one program) has been renamed to DupHMM.py
(2) Viterbi.exe was removed, as was all support for Windows in DupHMM.py
(3) All function names in python scripts were converted to all lower_case, as is the convention, instead of Upper_Case, which I often times used
(4) Added IGV screenshots for use in the DupHMM wiki in illustrating how to analyze DupHMM results files.
Note: DupHMM.py fractional copy state bug remains to be fixed.