First commit for GA4GH common classes and Picard runner

I'm more in favor of actually having a basic working version of the URL, in order to properly test-drive it.  Without it, we would not experience the benefits and how to improve it.  In any case, we will always have the option of a tabix/samtools/etc. approach as shown here:

http://davetang.org/muse/2013/02/22/using-tabix/