Add relative variant region to incorporateGFF

[chrismit]

Add the affected basepairs relative to the transcript in the incorporateGFF output.
So instead of:

CUFF.4455.3 1 235090392 A->AA;1 235089263 TGT->T

We have:

CUFF.4455.3 1 235090392(543) A->AA;1 235089263(354) TGT->T