38bc9e01ce6e7b22f0533c6624a64a17fd6c7bff
angie
  Fri Sep 27 17:20:54 2013 -0700
Major restructuring of gpFx.c, to accomodate large deletions thatcan 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

diff --git src/hg/inc/soTerm.h src/hg/inc/soTerm.h
index befac04..8d95550 100644
--- src/hg/inc/soTerm.h
+++ src/hg/inc/soTerm.h
@@ -1,30 +1,31 @@
 /* soTerm.h --- a subset of locally used Sequence Ontology terms */
 
 // To explore the full tree of SO terms and their relationships, try the MISO browser:
 // http://www.sequenceontology.org/browser/obob.cgi
 
 // would be nice to more closely match Ensembl's subset of SO:
 // http://uswest.ensembl.org/info/docs/variation/predicted_data.html#consequences
 
 #ifndef SOTERM_H
 #define SOTERM_H
 
 enum soTerm	// the various variant effects
     {
     regulatory_region_variant=1566,
     stop_retained_variant=1567,
+    exon_loss=1572,
     splice_acceptor_variant=1574,
     splice_donor_variant=1575,
     complex_transcript_variant=1577,
     stop_lost=1578,
     coding_sequence_variant=1580,
     initiator_codon_variant=1582,
     missense_variant=1583,
     stop_gained=1587,
     frameshift_variant=1589,
     nc_transcript_variant=1619,
     mature_miRNA_variant=1620,
     NMD_transcript_variant=1621,
     _5_prime_UTR_variant=1623,
     _3_prime_UTR_variant=1624,
     incomplete_terminal_codon_variant=1626,