0c882cb50cc196e069a5df0f19cb83997d6d3882
angie
  Tue Apr 16 14:00:17 2019 -0700
Added SO terms used in dbSNP b152 JSON, plus an soUnknown enum value for when no SO terms are assigned.
Move up nc_transcript_variant in funcImpactOrder to be above up/downstream.  refs #23283

diff --git src/hg/inc/soTerm.h src/hg/inc/soTerm.h
index 9446c96..8dbc8d2 100644
--- src/hg/inc/soTerm.h
+++ src/hg/inc/soTerm.h
@@ -1,71 +1,78 @@
 /* soTerm.h --- a subset of locally used Sequence Ontology terms */
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 // 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
     {
+    soUnknown=0,
+    frameshift=865,
     regulatory_region_variant=1566,
     stop_retained_variant=1567,
     exon_loss_variant=1572,
     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,
+    terminator_codon_variant=1590,
     nc_transcript_variant=1619,
     mature_miRNA_variant=1620,
     NMD_transcript_variant=1621,
     UTR_variant=1622,
     _5_prime_UTR_variant=1623,
     _3_prime_UTR_variant=1624,
     incomplete_terminal_codon_variant=1626,
     intron_variant=1627,
     intergenic_variant=1628,
     splice_site_variant=1629,
     splice_region_variant=1630,
     upstream_gene_variant=1631,
     downstream_gene_variant=1632,
     TF_binding_site_variant=1782,
     non_coding_transcript_exon_variant=1792,
     protein_altering_variant=1818,
     synonymous_variant=1819,
     inframe_indel=1820,
     inframe_insertion=1821,
     inframe_deletion=1822,
     feature_variant=1878,
     transcript_ablation=1893,
+    upstream_transcript_variant=1986,
+    downstream_transcript_variant=1987,
     no_sequence_alteration=2073,
+    genic_downstream_transcript_variant=2152,
+    genic_upstream_transcript_variant=2153,
     };
 
 char *soTermToString(enum soTerm termNumber);
 /* Translate termNumber to its string equivalent; errAbort if not found.
  * Do not modify or free result. */
 
 int soTermStringToId(char *soTermStr);
 /* Translate soTermStr into its numeric ID.  Return -1 if soTermStr is not recognized. */
 
 enum soTerm soTermStringIdToId(char *soIdStr);
 /* Given a string like "SO:0001627", parse out the numeric ID and convert to enum soTerm. */
 
 char *soTermToMisoLink(enum soTerm term);
 /* Return an HTML <a> link to the MISO browser page for term
  * (except if it's soUnknown, just return text not a link). */
 
 int soTermCmp(const void *a, const void *b);
 /* Compare two enum soTerms for sorting by descending order of functional impact. */
 
 #endif /* SOTERM_H */