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

diff --git src/hg/hgTracks/chainTrack.c src/hg/hgTracks/chainTrack.c
index 3146036..2fd8875 100644
--- src/hg/hgTracks/chainTrack.c
+++ src/hg/hgTracks/chainTrack.c
@@ -6,30 +6,31 @@
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "hash.h"
 #include "localmem.h"
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
 #include "chainBlock.h"
 #include "chainLink.h"
 #include "chainDb.h"
 #include "chainCart.h"
 #include "hgColors.h"
 #include "hubConnect.h"
+#include "chromAlias.h"
 
 
 
 struct cartOptions
     {
     enum chainColorEnum chainColor; /*  ChromColors, ScoreColors, NoColors */
     int scoreFilter ; /* filter chains by score if > 0 */
     };
 
 struct sqlClosure
 {
 struct sqlConnection *conn;
 };
 
 struct bbClosure
@@ -153,31 +154,31 @@
 
 void *closure;
 struct sqlClosure sqlClosure;
 struct bbClosure bbClosure;
 linkRetrieveFunc queryFunc;
 if (tg->isBigBed)
     {
     closure = &bbClosure;
     queryFunc = doBbQuery;
     char *fileName = trackDbSetting(tg->tdb, "linkDataUrl");
     if (fileName == NULL)
         {
         warn("Cannot find linkDataUrl in custom track \"%s\"\n", tg->shortLabel);
         return;
         }
-    struct bbiFile *bbi =  bigBedFileOpen(fileName);
+    struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
     if (bbi == NULL)
         return;
     bbClosure.bbi =  bbi;
     }
 else
     {
     closure = &sqlClosure;
     queryFunc = doQuery;
     sqlClosure.conn = hAllocConn(database);
     }
 
 lm = lmInit(1024*4);
 hash = newHash(0);
 
 /* Make up a hash of all linked features keyed by