Expanding on README
Adding version to usage statement. Saving some more nice output.
Fixing typo in usage message
Rearranging command line to be more consistent with other eap_runs. Moving set-path responsibility to this program so hotspot.py need not worry about it. Improving bigWig generation.
Uncommenting hotspot.py.  Removing more temp files.
Removing some no longer used arguments.
Merge branch 'master' of https://github.com/ENCODE-DCC/uniformAnalysis