Cram code base

Just rebased the branch from master. Briefly:
- adds new htsjdk.samtools.cram package that contains CRAM backend like codecs, structures and thins
- adds CRAM type in SamReader
- CRAMFileReader and writer implementations
- changed visibility of TagValueAndUnsignedArrayFlag, used in the cram package
fileName and os are never initialized. When a new CRAMFileWriter is instantiated all subsequent calls with return NPEs as a result.  There should probably be a constructor that can take a File or an OutputStream similar to BAMFileWriter.