23e3f7b1a4c78acd2198da73f4a4392290c51736
angie
  Fri Apr 19 16:12:24 2013 -0700
Added detection of many new SO terms to gpFx: {5,3} UTR, splice_{donor,acceptor},non_coding_exon, and very detailed coding change terms to match Ensembl e.g.
stop_retained_variant, NMD_transcript_variant). Also tweaks to annoFormatVep to
represent insertion positions the way they do.
TODO: lots more testing! and convert gpFx to use localmem.
refs #6152

diff --git src/hg/inc/soTerm.h src/hg/inc/soTerm.h
index ce5b21e..befac04 100644
--- src/hg/inc/soTerm.h
+++ src/hg/inc/soTerm.h
@@ -1,82 +1,47 @@
-/* soTerm.h --- Sequence Ontology terms and supporting data structures */
+/* 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,
     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,
     intron_variant=1627,
     intergenic_variant=1628,
     splice_region_variant=1630,
     upstream_gene_variant=1631,
     downstream_gene_variant=1632,
     TF_binding_site_variant=1782,
     non_coding_exon_variant=1792,
     protein_altering_variant=1818,
     synonymous_variant=1819,
     inframe_insertion=1821,
     inframe_deletion=1822,
     };
 
-struct soCall  // a single variant effect call
-    {
-    struct soCall *next;
-    char *transcript;		// ID of feature affected by this call
-    uint    soNumber;           // Sequence Ontology Number of effect
-    union
-	{
-	struct codingChange     // (non)synonymous variant, deletions in CDS
-	    {
-	    uint exonNumber;
-
-	    // the next three should have a length specified too
-	    uint cDnaPosition;		// offset of variant in transcript cDNA
-	    uint cdsPosition;		// offset of variant from transcript's cds start
-	    uint pepPosition;		// offset of variant in translated product
-	    char *aaOld;		// peptides, before change by variant (starting at pepPos)
-	    char *aaNew;		// peptides, changed by variant
-	    char *codonOld;		// codons, before change by variant (starting at cdsPos)
-	    char *codonNew;		// codons, changed by variant
-	    } codingChange;
-	struct     // intron_variant
-	    {
-	    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
-	    char    *soOther7;           // Ancillary detail 7
-	    } generic;
-	} sub;
-    };
-
 char *soTermToString(enum soTerm termNumber);
 /* Translate termNumber to its string equivalent.  Do not modify or free result. */
 
 #endif /* SOTERM_H */