CRAM container offsets should be updated by SAMFileMerger

[cmnbroad]

CRAM containers include a field that specifies the container's offset in the containing stream (intended use is to support read name regeneration during random access for compression modes that support not preserving read names). The value is currently written but not otherwise used by htsjdk, but may be used by other CRAM implementations, so the values should be updated when merging the parts by SAMFileMerger.