Nh pr 97

Please see pull-request #97.  This differs as follows:
* Squash commits from the individual committers.
* LICENSE file is no longer present in the history.
* Rebased on top of master.

As an aside, we release HTSJDK and Picard at the same time.  Therefore, I would be grateful to understand what I need to do to start publishing the HTSJDK release.  The release script we use can be found in Picard: https://github.com/broadinstitute/picard/blob/master/src/scripts/release_picard.sh