39df62e630e31c0f8019bb350d64736ebe44220d
angie
  Wed May 13 15:40:48 2020 -0700
oops, forgot to call hReplaceGbdb on new tree file for VCF (and on .vcf.gz file for that matter).  refs #25554

diff --git src/hg/hgTracks/vcfTrack.c src/hg/hgTracks/vcfTrack.c
index 7adba22..75140df 100644
--- src/hg/hgTracks/vcfTrack.c
+++ src/hg/hgTracks/vcfTrack.c
@@ -1253,31 +1253,31 @@
 if (hapHeight >= minHeightForLabels)
     drawSampleLabels(vcff, hvg, isAllDiploid, yOff+extraPixel, hapHeight, gtHapOrder, gtHapCount,
                      font, color, tg->track);
 else
     drawSampleTitles(vcff, yOff+extraPixel, hapHeight, gtHapOrder, gtHapCount, tg->track);
 }
 
 static struct phyloTree *getTreeFromFile(struct trackDb *tdb)
 /* Get the filename that follows trackDb setting 'hapClusterMethod treeFile ' and read it in
  * as a phyloTree. */
 {
 char *hapMethod = cloneString(trackDbSetting(tdb, VCF_HAP_METHOD_VAR));
 if (! startsWithWord(VCF_HAP_METHOD_TREE_FILE, nextWord(&hapMethod)))
     errAbort("getTreeFromFile: expected trackDb setting " VCF_HAP_METHOD_VAR "to start with '"
              VCF_HAP_METHOD_TREE_FILE "' followed by a file name, but got '%s'", hapMethod);
-char *fileName = nextWord(&hapMethod);
+char *fileName = hReplaceGbdb(nextWord(&hapMethod));
 return phyloOpenTree(fileName);
 }
 
 struct hash *makeSampleToIx(struct vcfFile *vcff)
 /* Alloc & return a hash of sample names to genotype indices in vcff. */
 {
 struct hash *sampleToIx = hashNew(0);
 int gtIx;
 for (gtIx = 0;  gtIx < vcff->genotypeCount;  gtIx++)
     hashAddInt(sampleToIx, vcff->genotypeIds[gtIx], gtIx);
 return sampleToIx;
 }
 
 static int gtIxFromSample(struct hash *sampleToIx, char *sample, char *vcfFileName)
 /* Look up sample's genotype index in sampleToIx, die complaining about vcfFileName if not found. */
@@ -1565,30 +1565,31 @@
 /* Figure out url or file name. */
 if (tg->parallelLoading)
     {
     /* do not use mysql during parallel-fetch load */
     fileOrUrl = trackDbSetting(tg->tdb, "bigDataUrl");
     }
 else
     {
     struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
     fileOrUrl = bbiNameFromSettingOrTableChrom(tg->tdb, conn, tg->table, chromName);
     hFreeConn(&conn);
     }
 
 if (isEmpty(fileOrUrl))
     return;
+fileOrUrl = hReplaceGbdb(fileOrUrl);
 int vcfMaxErr = -1;
 struct vcfFile *vcff = NULL;
 boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE);
 if (slCount(windows)>1)
     hapClustEnabled = FALSE;  // haplotype sorting display not currently available with multiple windows.
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     vcff = vcfTabixFileAndIndexMayOpen(fileOrUrl, tbiFileOrUrl, chromName, winStart, winEnd, vcfMaxErr, -1);
     if (vcff != NULL)
 	{
 	filterRecords(vcff, tg->tdb);
         int vis = tdbVisLimitedByAncestors(cart,tg->tdb,TRUE,TRUE);
 	if (hapClustEnabled && vcff->genotypeCount > 1 &&