The bug causing fractional copy state number to not work turned out to be due to a single line with int(variable), which has been changed to float(variable), as well as due to a Python bug which prevents OrderedDict from correctly ordering dictionary entries when a float key is given, which was thus affecting the proper ordering of copy number states. This was temporarily fixed by sorting the 'states' OrderedDict after creating it, although this may be removed once the bug is fixed. I also removed all references to the -R option, as DupHMM.py now assumes the user is running a Unix system and that R should thus be accessible via 'Rscript'.
DupHMM is now fully functional, packaged together, and ready to be downloaded by other users