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
refMd5 setter is never called so we get a NPE when we write a slice on line 66 of SliceIO.java

baos.write(s.refMD5);