b622d147b7dbac52dbf3ba26928cd18e02d42bd8
braney
  Sat Feb 26 12:34:37 2022 -0800
add support for using a bigBed as the chromAlias file

diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c
index b71a01b..5e1dc07 100644
--- src/hg/hgTracks/vcfTrack.c
+++ src/hg/hgTracks/vcfTrack.c
@@ -949,31 +949,31 @@
             }
         }
     }
 return txiList;
 }
 
 static struct txInfo *txInfoLoadBigGenePred(struct seqWindow *gSeqWin, struct trackDb *gTdb)
 /* Load up bigGenePred items in current window and make txInfo for each. */
 {
 struct txInfo *txiList = NULL;
 char *fileName = cloneString(trackDbSetting(gTdb, "bigDataUrl"));
 if (fileName == NULL)
     fileName = cloneString(trackDbSetting(gTdb, "bigGeneDataUrl"));
 if (isNotEmpty(fileName))
     {
-    struct bbiFile *bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasChromToAliasHash(database));
+    struct bbiFile *bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasFindAliases);
     struct lm *lm = lmInit(0);
     struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chromName, winStart,
                                                         winEnd, 0, lm);
     struct bigBedInterval *bb;
     for (bb = bbList; bb != NULL; bb = bb->next)
         {
         struct genePredExt *gp = genePredFromBigGenePred(chromName, bb);
         struct txInfo *txi = txInfoFromGenePred((struct genePred *)gp, gSeqWin);
         slAddHead(&txiList, txi);
         }
     bbiFileClose(&bbi);
     lmCleanup(&lm);
     }
 return txiList;
 }