c72b4b4412c574336911c4eb7135a9677c2773ef
braney
  Wed Apr 25 14:07:45 2012 -0700
ongoing #6152.   Added support for variants longer than 1 in CDS.
diff --git src/hg/inc/soterm.h src/hg/inc/soterm.h
index 4776bf9..c436a37 100644
--- src/hg/inc/soterm.h
+++ src/hg/inc/soterm.h
@@ -1,72 +1,74 @@
 /* soterm.h --- Sequence Ontology terms and supporting data structures */
 
 #ifndef SOTERM_H
 #define SOTERM_H
 
 enum 	// the various variant effects
     {
     regulatory_region_variant=1566,
     stop_retained_variant=1567,
     splice_acceptor_variant=1574,
     splice_donor_variant=1575,
     Complex_transcript_variant=1577,
     stop_lost=1578,
     coding_sequence_variant=1580,
     initiator_codon_variant=1582,
     missense=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,
     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_synonymous_variant=1818,
     synonymous_variant=1819,
     } soTerm;
 
 struct soCall  // a single variant effect call
     {
     struct soCall *next;
     uint    soNumber;           // Sequence Ontology Number
     union
 	{
 	struct codingChange     // (non)synonymous variant
 	    {
 	    char *transcript;
 	    uint exonNumber;
+
+	    // the next three should have a length specified too
 	    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;
     };
 
 #endif /* SOTERM_H */