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

diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c
index c911968..9ebe36b 100644
--- src/hg/hgTracks/vcfTrack.c
+++ src/hg/hgTracks/vcfTrack.c
@@ -14,30 +14,31 @@
 #include "hdb.h"
 #include "hgColors.h"
 #include "hgTracks.h"
 #include "iupac.h"
 #include "net.h"
 #include "pgSnp.h"
 #include "phyloTree.h"
 #include "trackHub.h"
 #include "trashDir.h"
 #include "variantProjector.h"
 #include "vcf.h"
 #include "vcfUi.h"
 #include "knetUdc.h"
 #include "udc.h"
 #include "memgfx.h"
+#include "chromAlias.h"
 
 // Russ Corbett-Detig suggested darker shades for coloring non-synonymous variants green
 Color darkerShadesOfGreenOnWhite[EXPR_DATA_SHADES];
 
 static boolean getMinQual(struct trackDb *tdb, double *retMinQual)
 /* Return TRUE and set retMinQual if cart contains minimum QUAL filter */
 {
 if (cartOrTdbBoolean(cart, tdb, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL))
     {
     if (retMinQual != NULL)
 	*retMinQual = cartOrTdbDouble(cart, tdb, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL);
     return TRUE;
     }
 return FALSE;
 }
@@ -948,31 +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 = bigBedFileOpen(hReplaceGbdb(fileName));
+    struct bbiFile *bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasGetHash(database));
     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;
 }