4a913761c86409e1bb5972b7667ff5d3b8e7b081
hiram
  Tue Nov 5 15:19:51 2013 -0800
compare chrom names case dependent refs #11907
diff --git src/hg/genePredCheck/genePredCheck.c src/hg/genePredCheck/genePredCheck.c
index 45a03e4..1a714f0 100644
--- src/hg/genePredCheck/genePredCheck.c
+++ src/hg/genePredCheck/genePredCheck.c
@@ -32,38 +32,46 @@
   "options:\n"
   "   -db=db - If specified, then this database is used to\n"
   "    get chromosome sizes, and perhaps the table to check.\n"
   "\n");
 }
 
 static void checkAGenePred(char *fileTbl, int iRec, struct genePred *gp)
 /* check one genePred */
 {
 int chromSize = -1;  /* default to not checking */
 char desc[512];
 
 safef(desc, sizeof(desc), "%s:%d", fileTbl, iRec);
 if (gDb != NULL)
     {
+    // hGetChromInfo is case independent
     struct chromInfo *ci = hGetChromInfo(gDb, gp->chrom);
     if (ci == NULL)
         {
         fprintf(stderr, "Error: %s: %s has invalid chrom for %s: %s\n",
                 desc, gp->name, gDb, gp->chrom);
         gErrCount++;
         chromSize = -1;  // don't validate
         }
+    else if (differentString(gp->chrom, ci->chrom)) // verify case dependent ==
+        {
+        fprintf(stderr, "Error: %s: %s has invalid chrom for %s: %s\n",
+                desc, gp->name, gDb, gp->chrom);
+        gErrCount++;
+        chromSize = -1;  // don't validate
+        }
     else
         chromSize = ci->size;
     }
 gErrCount += genePredCheck(desc, stderr, chromSize, gp);
 gChkCount++;
 }
 
 static void checkGenePred(char *fileTbl)
 /* check a genePred file or table */
 {
 struct sqlConnection *conn = NULL;
 struct genePredReader *gpr;
 struct genePred *gp;
 int iRec = 0;