August 2014 bugs

@bradnerComputation Charles, please review these changes resolving #30  and #29 .  This also fixes other minor items and provides a couple new optional arguments -- please see commit comments for more details.

I added several automated tests to verify the changes.

If possible, please ask someone to spend some time manually testing this.  Now that we are at version 1.0 and will be publishing a paper highlighting the tool, I hope we can have some confidence in this code.  I really don't want to be supplying a tool that gives misleading results to researchers, and testing and thorough code review could go a long way in improving the quality.

Thanks.