e49078c13bb3c9243511050a99f54455db3aa1b8
angie
  Fri Aug 12 16:24:48 2016 -0700
Mapping of SO terms to SO IDs was in snp125Ui.c but really should be in soTerm.c.  soTerm was updated to include intergenic_variant but snp125Ui was not (HT Christopher Lee).  Now snp125Ui still maps dbSNP func terms to SO terms, but the term string to ID mapping is all in soTerm now.  refs #17209

diff --git src/hg/inc/soTerm.h src/hg/inc/soTerm.h
index 3ef3f54..dcaa43f 100644
--- src/hg/inc/soTerm.h
+++ src/hg/inc/soTerm.h
@@ -1,51 +1,54 @@
 /* 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
     {
     regulatory_region_variant=1566,
     stop_retained_variant=1567,
     exon_loss=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,
     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,
     };
 
 char *soTermToString(enum soTerm termNumber);
 /* Translate termNumber to its string equivalent.  Do not modify or free result. */
 
+int soTermStringToId(char *soTermStr);
+/* Translate soTermStr into its numeric ID.  Return -1 if soTermStr is not recognized. */
+
 #endif /* SOTERM_H */