91c7dfbd21a1418f9030314f86719672fa33e6dd
chinhli
  Wed Sep 21 11:41:18 2011 -0700
Complete switch over to use bigBed trick
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index b342e6e..9f6a55a 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -9766,31 +9766,31 @@
 		printf("<B>Related UCSC Gene(s): </B>");
 	    else
 		printf(", ");
     	    printf("<A HREF=\"%s%s&hgg_chrom=none\">", "../cgi-bin/hgGene?hgg_gene=", row[0]);
     	    printf("%s</A></B>", row[0]);
 	    printedCnt++;
 	    }
         if (printedCnt >= 1) printf("<BR>\n");
 	}
     sqlFreeResult(&sr);
 
     // show GeneReviews  link(s)
     if (sqlTablesExist(conn, "geneReviewsRefGene"))
         {
         safef(query, sizeof(query),
-          "select distinct r.name2 from refLink l, mim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s",
+          "select distinct r.name2 from refLink l, omim2gene g, refGene r where l.omimId=%s and g.geneId=l.locusLinkId and g.entryType='gene' and chrom='%s' and txStart = %s and txEnd= %s",
         itemName, chrom, chromStart, chromEnd);
         sr = sqlMustGetResult(conn, query);
         if (sr != NULL)
             {
             while ((row = sqlNextRow(sr)) != NULL)
                 {
                 prGRShortRefGene(row[0]);
                 }
             }
         sqlFreeResult(&sr);
         }
 
     }
 
 printf("<HR>");
@@ -23855,37 +23855,41 @@
 {
 struct sqlConnection *conn = hAllocConn(database);
 //char *table = tdb->table;
 int start = cartInt(cart, "o");
 int num = 4;
 
  genericHeader(tdb, itemName);
  genericBedClick(conn, tdb, itemName, start, num);
  prGeneReviews(conn, itemName);
  printf("<BR>");
  printTrackHtml(tdb);
  hFreeConn(&conn);
 }
 
 void prGeneReviews(struct sqlConnection *conn, char *itemName)
-/* print GeneReviews associated to this item */
+/* print GeneReviews associated to this item 
+   Note: this print function has been replaced by addGeneReviewToBed.pl
+         which print the same information to the field 5 of bigBed file
+*/ 
+         
 {
 struct sqlResult *sr;
 char **row;
 char query[512];
 int i;
-char *clickMsg = "Click 'Short name' link below to search GeneReviews";
+char *clickMsg = "Click link(s) below to search GeneReviews and GeneTests";
 boolean firstTime = TRUE;
 
 safef(query, sizeof(query), "select  grShort, diseaseID, diseaseName from geneReviewsRefGene where geneSymbol='%s'", itemName);
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
         char *grShort = *row++;
         char *diseaseID = *row++;
         char *diseaseName = *row++;
 
 
         if (firstTime)
         {
           printf("<BR><B> GeneReview(s) available for %s:</B> (%s)<BR>",itemName,clickMsg);
           firstTime = FALSE;
@@ -25154,31 +25158,31 @@
     {
     doT2gDetails(tdb, item);
     }
 else if (tdb != NULL && startsWith("bedDetail", tdb->type))
     {
     doBedDetail(tdb, NULL, item);
     }
 else if (startsWith("numtS", table))
     {
     doNumtS(tdb, item);
     }
 else if (startsWith("cosmic", table))
     {
     doCosmic(tdb, item);
     }
-else if (startsWith("geneReviews", table))
+else if (sameString("geneReviews", table))
     {
     doGeneReviews(tdb, item);
     }
 else if (tdb != NULL)
     {
     genericClickHandler(tdb, item, NULL);
     }
 else
     {
     cartWebStart(cart, database, "%s", track);
     printf("Sorry, clicking there doesn't do anything yet (%s).", track);
     }
 /* End of 1000+ line dispatch on table involving 100+ if/elses. */
 
 if (didCartHtmlStart)