Should we make printing this optional? If someone runs this against a whole genome, they'll get nearly a billion lines of output.

Two options for make it optional: (1) add a commandline option or (2), if this is useful for debugging only, extend the "logging" class and use log.info("...") or log.debug("...").

This is your feature so you know it better than I. If users need this output then please ignore this suggestion.