0c1bec334a6ee21c9b662d8e81e689b668fb4467
fanhsu
  Tue Mar 8 08:45:56 2011 -0800
Updated funtions for new OMIM tracks.
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 3bcc5b9..069157e 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9796,73 +9796,78 @@
 char *title2 = NULL;
 char *chrom, *chromStart, *chromEnd;
 char *omimId;
 char *avId;
 char *dbSnpId;
 char *chp;
 char *seqId = NULL;
 char avString[255];
 char *avDesc = NULL;
 
 chrom      = cartOptionalString(cart, "c");
 chromStart = cartOptionalString(cart, "o");
 chromEnd   = cartOptionalString(cart, "t");
 
 avId = strdup(itemName);
+safef(avString, sizeof(avString), "%s", itemName);
 
 chp = strstr(itemName, ".");
 *chp = '\0';
 omimId = strdup(itemName);
 
+chp = avString;
+chp = strstr(avString, ".");
+*chp = '#';
+
 if (url != NULL && url[0] != 0)
     {
-    printf("<B>OMIM Entry ");fflush(stdout);
-    printf("<A HREF=\"%s%s\" target=_blank>", url, itemName);
-    printf("%s</A></B>", itemName);
     safef(query, sizeof(query),
     	  "select title1, title2,  format(seqNo/10000,4), v.description from omimGeneMap m, omimAv v where m.omimId=%s and m.omimId=v.omimId and v.avId='%s';", itemName, avId);
 
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
     	{
 	seqId = strdup(row[2]);
-	safef(avString, sizeof(avString), "%s#%s", omimId, seqId+2L);
 	if (row[0] != NULL)
 	    {
 	    title1 = cloneString(row[0]);
-    	    printf(": %s", title1);
 	    }
 	if (row[1] != NULL)
 	    {
 	    title2 = cloneString(row[1]);
-    	    printf(" %s ", title2);
 	    }
-	avDesc = row[3];
+	avDesc = cloneString(row[3]);
 	}
     sqlFreeResult(&sr);
     
+    printf("<B>OMIM Allelic Variant: ");
+    printf("<A HREF=\"%s%s\" target=_blank>", url, avString);
+    printf("%s</A></B>", avId);
+    printf(" %s", avDesc);
+
+    printf("<BR><B>OMIM Entry ");
+    printf("<A HREF=\"%s%s\" target=_blank>", url, itemName);
+    printf("%s</A></B>", itemName);
+    if (title1 != NULL) printf(": %s", title1);
+    if (title2 != NULL) printf(" %s ", title2);
+    
     printf("<BR>\n");
     printf("<B>OMIM page at NCBI: ");
     printf("<A HREF=\"%s%s\" target=_blank>", ncbiOmimUrl, itemName);
     printf("%s</A></B><BR>", itemName);
 
-    printf("<B>Allelic Variant: ");fflush(stdout);
-    printf("<A HREF=\"%s%s\" target=_blank>", url, avString);
-    printf("%s</A></B>", avId);
-    printf(" %s", avDesc);
-
     safef(query, sizeof(query),
     	  "select replStr from omimAvRepl where avId=%s;", avId);
     sr = sqlMustGetResult(conn, query);
     row = sqlNextRow(sr);
     if (row != NULL)
     	{
 	if (row[0] != NULL)
 	    {
 	    char *replStr;
 	    replStr= cloneString(row[0]);
     	    printf("<BR><B>Amino Acid Replacement:</B> %s\n", replStr);
 	    }
 	}
     sqlFreeResult(&sr);
 
@@ -23815,31 +23820,31 @@
     {
     doSwitchDbTss(tdb, item);
     }
 else if (sameWord(table, "omimLocation"))
     {
     doOmimLocation(tdb, item);
     }
 else if (sameWord(table, "omimAvSnp"))
     {
     doOmimAvSnp(tdb, item);
     }
 else if (sameWord(table, "omimGeneClass2"))
     {
     doOmimGeneClass3(tdb, item);
     }
-else if (sameWord(table, "omimGeneClass3"))
+else if (sameWord(table, "omimGene2"))
     {
     doOmimGeneClass3(tdb, item);
     }
 else if (sameWord(table, "omimAv"))
     {
     doOmimAv(tdb, item);
     }
 else if (sameWord(table, "rgdGene"))
     {
     doRgdGene(tdb, item);
     }
 else if (sameWord(table, "rgdGene2"))
     {
     doRgdGene2(tdb, item);
     }