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.
From our earlier conversations with Heng I'm pretty sure the original docs at the top of the file were correct:
- so a read has a primary alignment and secondary alignments are alternate mappings
- for each of those possible alignments, if its chimeric, then it also gets a supplementary alignment
- and we chose for v0.5 to have GAReadAlignment be a flattened representation of all of those things (with the ability to get more complex in later versions)

thankfully, in a lot of data there is only one alignment per read, which makes things easier to understand. (of course I know there are plenty of exceptions :)