CRAM in name-sorted order & reference

[jkbonfield]

Name sorted data in CRAM requires random access on the reference in order to achieve reference based compression. While still small, this isn't so efficient in memory usage nor perhaps in CPU.

Consider making the default option of "no_ref" when outputting name sorted data, with an additional "ref" option permitted to actively force reference compression on again.

See #502 for some background info.