Update alignment docs

This is my follow on to #95; it'll need to be rebased after #95 merges before it can be merged in.

This provides more explicit definitions for the supplementary/secondary alignment flags, the cigar operators, and some of the alignment specific fields.
We should maybe add a comment to alignment field to replace the deleted sentence?
"This field will exist if the read was mapped and this is not a secondary nor supplementary alignment." (or something like that)