04c67a0e7bcb65c217598e5e44084bf4c5c0674d
angie
  Tue Mar 5 12:16:10 2013 -0800
Feature #6152 (Variant Annotation Integrator): first cut of annoFormatVep whichproduces output in the format of Ensembl's Variant Effect Predictor (VEP), along
with modifications to soTerm, gpFx and annoGratorGpVar to enable VEP-like output.

diff --git src/hg/lib/soTerm.c src/hg/lib/soTerm.c
new file mode 100644
index 0000000..73bf437
--- /dev/null
+++ src/hg/lib/soTerm.c
@@ -0,0 +1,43 @@
+/* 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 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
+}