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/lib/soTerm.c src/hg/lib/soTerm.c
index 73bf437..9dc9f8e 100644
--- src/hg/lib/soTerm.c
+++ src/hg/lib/soTerm.c
@@ -1,43 +1,44 @@
 /* soTerm - Sequence Ontology terms that we use for compatibility with Ensembl & others. */
 
 #include "common.h"
 #include "soTerm.h"
 
 char *soTermToString(enum soTerm termNumber)
 /* Translate termNumber to its string equivalent.  Do not modify or free result. */
 {
 switch (termNumber)
     {
     case regulatory_region_variant : return "regulatory_region_variant"; break;
     case stop_retained_variant : return "stop_retained_variant"; break;
+    case exon_loss : return "exon_loss"; break;
     case splice_acceptor_variant : return "splice_acceptor_variant"; break;
     case splice_donor_variant : return "splice_donor_variant"; break;
     case complex_transcript_variant : return "complex_transcript_variant"; break;
     case stop_lost : return "stop_lost"; break;
     case coding_sequence_variant : return "coding_sequence_variant"; break;
     case initiator_codon_variant : return "initiator_codon_variant"; break;
     case missense_variant : return "missense_variant"; break;
     case stop_gained : return "stop_gained"; break;
     case frameshift_variant : return "frameshift_variant"; break;
     case nc_transcript_variant : return "nc_transcript_variant"; break;
     case mature_miRNA_variant : return "mature_miRNA_variant"; break;
     case NMD_transcript_variant : return "NMD_transcript_variant"; break;
     case _5_prime_UTR_variant : return "5_prime_UTR_variant"; break;
     case _3_prime_UTR_variant : return "3_prime_UTR_variant"; break;
     case incomplete_terminal_codon_variant : return "incomplete_terminal_codon_variant"; break;
     case intron_variant : return "intron_variant"; break;
     case intergenic_variant : return "intergenic_variant"; break;
     case splice_region_variant : return "splice_region_variant"; break;
     case upstream_gene_variant : return "upstream_gene_variant"; break;
     case downstream_gene_variant : return "downstream_gene_variant"; break;
     case TF_binding_site_variant : return "TF_binding_site_variant"; break;
     case non_coding_exon_variant : return "non_coding_exon_variant"; break;
     case protein_altering_variant : return "protein_altering_variant"; break;
     case synonymous_variant : return "synonymous_variant"; break;
     case inframe_deletion : return "inframe_deletion"; break;
     case inframe_insertion : return "inframe_insertion"; break;
     default:
 	errAbort("soTermToString: don't recognize term %u", termNumber);
     }
 return "ERROR"; // never get here
 }