Merge pull request #1 from iliat/master

First commit for GA4GH common classes and Picard runner
HTSJDK SamReader implementation using the API and example of its usage
Added ant build and updated HTSJDK
Addressing comments
Addressing comments 2
Merge pull request #2 from iliat/htsjdk-work

HTSJDK SamReader implementation using the API and example of its usage
Make sequence specification optional
Merge pull request #3 from iliat/htsjdk-work

Make sequence specification optional
Fix url format display