f7c4de416fe14ebd715a9595887dd5c84bd334e4
fanhsu
  Tue May 17 14:02:50 2011 -0700
Updated new OMIM tracks processing to use the new omimPhenotype table.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index f5fabbc..6b1b65c 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9436,54 +9436,51 @@
     safef(query, sizeof(query),
 	  "select k.transcript from knownCanonical k where k.chrom='%s' and k.chromStart=%s and k.chromEnd=%s",
 	  chrom, chromStart, chromEnd);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
     	{
 	kgId = cloneString(row[0]);
 	}
     sqlFreeResult(&sr);
 
     /* use geneSymbol from omimMorbidMap if available */
     if (geneSymbol!= NULL)
     	{
 	boolean disorderShown;
-	char *phenotypeClass, *questionable, *hasBracket, *hasBrace, *phenotypeId, *disorder;
+	char *phenotypeClass, *phenotypeId, *disorder;
 
 	printf("<B>Gene symbol(s):</B> %s", geneSymbol);
 	printf("<BR>\n");
 
 	/* display disorder for genes in morbidmap */
     	safef(query, sizeof(query),
-	 "select disorder, phenotypeClass, questionable, hasBracket, hasBrace, phenotypeId from omimDisorderPhenotype where omimId=%s order by disorder",
+	      "select description, phenotypeClass, phenotypeId from omimPhenotype where omimId=%s order by description",
 	 itemName);
     	sr = sqlMustGetResult(conn, query);
 	disorderShown = FALSE;
         while ((row = sqlNextRow(sr)) != NULL)
     	    {
 	    if (!disorderShown)
 	    	{
  		printf("<B>Disorder(s):</B><UL>\n");
 		disorderShown = TRUE;
 		}
 	    disorder       = row[0];
 	    phenotypeClass = row[1];
-	    questionable   = row[2];
-	    hasBracket     = row[3];
-	    hasBrace	   = row[4];
-	    phenotypeId    = row[5];
+	    phenotypeId    = row[2];
 	    printf("<LI>%s", disorder);
  	    if (phenotypeId != NULL)
 	    	{
 		if (!sameWord(phenotypeId, "-1"))
 		    {
                     printf(" (phenotype <A HREF=\"%s%s\" target=_blank>", url, phenotypeId);
                     printf("%s</A></B>)", phenotypeId);
 		    }
 		}
 	    printf("<BR>\n");
 	    }
 	if (disorderShown) printf("</UL>\n");
     	sqlFreeResult(&sr);
 	}
     else
@@ -9646,52 +9643,49 @@
 	    }
 	}
     sqlFreeResult(&sr);
 
     printf("<BR>\n");
     safef(query, sizeof(query),
     	  "select geneSymbol from omimGeneMap where omimId=%s;", itemName);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
     	{
 	geneSymbol = cloneString(row[0]);
 	}
     sqlFreeResult(&sr);
 
-    safef(query, sizeof(query),"select omimId from omimDisorderPhenotype where omimId=%s\n", omimId);
+    safef(query, sizeof(query),"select omimId from omimPhenotype where omimId=%s\n", omimId);
     if (sqlQuickNum(conn, query) > 0)
     	{
-	char *phenotypeClass, *questionable, *hasBracket, *hasBrace, *phenotypeId, *disorder;
+	char *phenotypeClass, *phenotypeId, *disorder;
 
 	printf("<B>Gene symbol(s):</B> %s", geneSymbol);
 	printf("<BR>\n");
 
 	/* display disorder for genes in morbidmap */
     	safef(query, sizeof(query),
-	 "select disorder, phenotypeClass, questionable, hasBracket, hasBrace, phenotypeId from omimDisorderPhenotype where omimId=%s order by disorder",
+	 "select description, phenotypeClass, phenotypeId from omimPhenotype where omimId=%s order by description",
 	 itemName);
     	sr = sqlMustGetResult(conn, query);
  	printf("<B>Disorder(s):</B><UL>\n");
         while ((row = sqlNextRow(sr)) != NULL)
     	    {
 	    disorder       = row[0];
 	    phenotypeClass = row[1];
-	    questionable   = row[2];
-	    hasBracket     = row[3];
-	    hasBrace	   = row[4];
-	    phenotypeId    = row[5];
+	    phenotypeId    = row[2];
 	    printf("<LI>%s", disorder);
  	    if (phenotypeId != NULL)
 	    	{
 		if (!sameWord(phenotypeId, "-1"))
 		    {
                     printf(" (phenotype <A HREF=\"%s%s\" target=_blank>", url, phenotypeId);
                     printf("%s</A></B>)", phenotypeId);
 		    }
 		}
 	    printf("<BR>\n");
 	    }
 	printf("</UL>\n");
     	sqlFreeResult(&sr);
 	}
     else