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/inc/soterm.h src/hg/inc/soterm.h
deleted file mode 100644
index e5baaa3..0000000
--- src/hg/inc/soterm.h
+++ /dev/null
@@ -1,74 +0,0 @@
-/* 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, deletions in CDS
-	    {
-	    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 */