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.
I think the result of past convos was a messy but viable solution like:

r1: main alignment {secondary: false, supplementary: false}
r2: chimeric data for main alignment {secondary: false, supplementary: true}
r3: alternate alignment {secondary: true, supplementary: false}
r4: chimeric data for alternate alignment {secondary: true, supplementary: true}

where all of those read alignments share the same fragment info and readNumber