Major restructuring of gpFx.c, to accomodate large deletions that
can knock out entire exons.  Now, instead of iterating through
exons and building a new genePred along with a sequence that has
one exon's modification, we project the variant start and end onto
cDNA and CDS coords up front.  Then there is only one modification
to make per allele, and in fact we only care about the actual
modification when there's a CDS change.
A new SO term, exon_loss, has been incorporated into gpFx and
hgVai's/annoGratorGpVar's filtering.
fixes #11771
Code review feedback, thanks Tim.
refs #11800
Release log update
Encode release log update
allMis1 doesn't have refGene so it can be used to make the upstream
files
Merge remote-tracking branch: upstream/master