54406b80d5d435970989acff7b22dd6146c6b411
braney
  Sat Jan 22 15:24:59 2022 -0800
adding chrom alias support to big files

diff --git src/hg/hgc/mafClick.c src/hg/hgc/mafClick.c
index 021618b..5b78f77 100644
--- src/hg/hgc/mafClick.c
+++ src/hg/hgc/mafClick.c
@@ -5,30 +5,31 @@
 
 #include "common.h"
 #include "hash.h"
 #include "linefile.h"
 #include "hgc.h"
 #include "maf.h"
 #include "obscure.h"
 #include "cheapcgi.h"
 #include "genePred.h"
 #include "botDelay.h"
 #include "hgMaf.h"
 #include "hui.h"
 #include "hCommon.h"
 #include "hubConnect.h"
 #include "trackHub.h"
+#include "chromAlias.h"
 
 extern boolean issueBotWarning;
 
 #define ADDEXONCAPITAL
 
 /* Javascript to help make a selection from a drop-down
  * go back to the server. */
 static char *autoSubmit = "document.gpForm.submit();";
 
 static void blueCapWrite(FILE *f, char *s, int size, char *r)
 /* Write capital letters in blue. */
 {
 boolean isBlue = FALSE;
 int i;
 for (i=0; i<size; ++i)
@@ -529,31 +530,31 @@
 	{
 	if (!cartVarExists(cart, buffer) && (speciesTarget != NULL))
 	    useTarg = TRUE;
 	else
 	    {
 	    char *val;
 
 	    val = cartUsualString(cart, buffer, "useCheck");
             useTarg = sameString("useTarg",val);
             }
         }
 
     if (sameString(tdb->type, "bigMaf"))
         {
         char *fileName = trackDbSetting(tdb, "bigDataUrl");
-        struct bbiFile *bbi = bigBedFileOpen(fileName);
+        struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
         mafList = bigMafLoadInRegion(bbi, seqName, winStart, winEnd);
         }
     else
         mafList = mafOrAxtLoadInRegion2(conn,conn2, tdb, seqName, winStart, winEnd,
                                         axtOtherDb, fileName);
     safef(dbChrom, sizeof(dbChrom), "%s.%s", hubConnectSkipHubPrefix(database), seqName);
 
     safef(option, sizeof(option), "%s.speciesOrder", tdb->track);
     speciesOrder = cartUsualString(cart, option, NULL);
     if (speciesOrder == NULL)
 	speciesOrder = trackDbSetting(tdb, "speciesOrder");
 
     int speciesCt = 0;
     char *species[2048];
     struct mafComp **newOrder;