testing for flag parameters explicitly returns true or false
simplified logic for testing taxon assignment
Added in python stdlib logging rather than just printing to screen
Fixed a bug where an expection is thrown if the root directory doesn't exist
make sure that the final OTUs are clustered at 99%
Fixed a couple of filepath errors that caused some files to be put in the wrong directory
Merge branch 'master' of github.com:ctSkennerton/Amplishot