JSON breaking schema changes

[davmlaw]

We don't want to break the schema (and wreck backwards compatability), but if we ever do, we should change a few things while we can. I'm going to document them here:

Change

• exons should be key/values as then we can add fields without breaking code that expects fixed length arrays

Add

• Support for phasing (see CDS phase (offset for eg ribo slippage) #76) - if we do the key/values above, just add this

[tedil]

Maybe also rename cds_{start,end} to tx_{start,end}?

[davmlaw]

@tedil cds is def coding start/end. Transcript extents are in the exons, so:

tx_start = exons[0][0]
tx_end = exons[-1][1]