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/hgc/hgc.c src/hg/hgc/hgc.c
index 6601eec..97cb8fb 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -17509,31 +17509,32 @@
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     char *gene = row[0];
     char *geneName = getSymbolForGeneName(geneTable, gene);
     int start = sqlUnsigned(row[1]);
     char *strand = row[2];
     boolean isRc = strand[0] == '-';
     printf(firstTwoColumnsPctS "%s (%d bases %sstream)</TD></TR>\n",
 	   geneTrack, geneName, snpMisoLinkFromFunc(isRc ? "near-gene-3" : "near-gene-5"),
 	   (start - snpEnd + 1), (isRc ? "down" : "up"));
     nearCount++;
     }
 sqlFreeResult(&sr);
 if (nearCount == 0)
-    printf("<TR><TD>%s&nbsp;&nbsp;</TD><TD></TD><TD>intergenic</TD></TR>", geneTrack);
+    printf("<TR><TD>%s&nbsp;&nbsp;</TD><TD></TD><TD>%s</TD></TR>", geneTrack,
+           snpMisoLinkFromFunc("intergenic_variant"));
 }
 
 static struct genePred *getGPsWithFrames(struct sqlConnection *conn, char *geneTable,
 					 char *chrom, int start, int end)
 /* Given a known-to-exist genePred table name and a range, return
  * genePreds in range with exonFrames populated. */
 {
 struct genePred *gpList = NULL;
 boolean hasBin;
 struct sqlResult *sr = hRangeQuery(conn, geneTable, chrom, start, end, NULL, &hasBin);
 struct sqlConnection *conn2 = hAllocConn(database);
 boolean hasFrames = (sqlFieldIndex(conn2, geneTable, "exonFrames") == hasBin + 14);
 char **row;
 while ((row = sqlNextRow(sr)) != NULL)
     {