Conflicts: public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
*NOTE: This commit has not been compiled!
* Includes tests that include HardClip to Read and Reference Coords. * Changed ReadUtils.HardClipByReferenceCoordinates from private to protected to allow for testing
Mauricio Carneiro
Roger Zurawicki