3ec9dec14cfbbe94f51eb94dd0cc861cad375f97
braney
  Tue Apr 17 18:58:18 2012 -0700
ongoing work on #6152.   Now with non-synonymous changes!  (well, at least with respect to the genomic DNA)
diff --git src/hg/inc/soterm.h src/hg/inc/soterm.h
index 8cd9abc..e44e333 100644
--- src/hg/inc/soterm.h
+++ src/hg/inc/soterm.h
@@ -19,41 +19,51 @@
     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,
     intron_variant=1627,
     intergenic_variant=1628,
     splice_region_variant=1630,
     upstream_gene_variant=1631,
     downstream_gene_variant=1632,
     inframe_deletion=1651,
     inframe_insertion=1652,
     TF_binding_site_variant=1782,
     non_coding_exon_variant=1792,
-    non_synonyous_variant=1818,
+    non_synonymous_variant=1818,
     synonymous_variant=1819,
     } soTerm;
 
 struct soCall  // a single variant effect call
     {
     struct soCall *next;
     uint    soNumber;           // Sequence Ontology Number
     union
 	{
-	struct     // a variant in an intron
+	struct     // (non)synonymous variant
+	    {
+	    char *transcript;
+	    uint exonNumber;
+	    uint cDnaPosition;
+	    uint cdsPosition;
+	    uint pepPosition;
+	    char *aaChanges;
+	    char *codonChanges;
+	    } codingChange;
+	struct     // intron_variant
 	    {
 	    char *transcript;
 	    uint intronNumber;
 	    } intron;
 	struct    // a generic variant
 	    {
 	    char    *soOther0;           // Ancillary detail 0
 	    char    *soOther1;           // Ancillary detail 1
 	    char    *soOther2;           // Ancillary detail 2
 	    char    *soOther3;           // Ancillary detail 3
 	    char    *soOther4;           // Ancillary detail 4
 	    char    *soOther5;           // Ancillary detail 5
 	    char    *soOther6;           // Ancillary detail 6
 	    } generic;
 	} sub;