Upgraded to v1beta2

Few comments on the migration:

* The flags field wasn't added back to the ReadsRDD. 
* As part of the migration utils-java was also upgraded, and the RetryPolicy removed.
* Also sneaked in a change to make applicationName='spark-examples' instead of the class name, so not every example needs to be authorized.

Fix #50 
Making the cigar from the Read object code should definitely move into utils, cause its specific to google genomics and thankfully it doesn't have any htsjdk dependencies.

(The comment on #50 was about applying-cigar-to-sequence code, and that hopefully someone else has coded up)