Master rebase and fixups for deprecations.
initial cram code base commit
added lossy options to CRAMFileWriter;
force lossless mode by default if no policies are given
lazy init of qs preservation with "*8"
Updated htsjdk to use SamReader instead of the deprecated SAMFileReader.
Also fixed a bug in the tlen calculation for cram compression records.
Master rebase and fixups for deprecations.