Adding utilities for read trimming.
Merge pull request #248 from fnothaft/read-trimming

Adding utilities for read trimming.
Adding ADAM to SAM conversion.
Adding failing test for SAM->ADAM round-trip

Adding a round-trip test which fails (at the moment) with an NPE -- I *think* this is
related to the failure to write out the RG tags?
Making updates to clean up failing test provided by Timothy.