overhauling alignment event classification and annotation

[jsaquing]

jotting ideas down to revisit later

• may be beneficial to align transcripts first, classify splicing events, then "push" ORF through transcript alignment to obtain protein-level event classifications?
  • calling frameshifts is probably still easier using the current method, so maybe a hybrid approach is necessary
  • however, I think this alternate method will greatly simplify classification of N- and C-terminal events
• should incorporate junctions into event classification somehow
  • automatically infer which junctions are "responsible" for an event?
• need some kind of enum or class hierarchy system for the different event types (e.g. exon skipping, alternative TIS, etc.)
  • store location information (i.e. which exons and junctions are involved in an event)

[jsaquing]

merging from #93

Jared had the idea of structuring the annotations of N-term/AS/C-term events as objects themselves. The primative annotations "build up" to the mid-level annotations.