8933db12a9efed4981ada1fcc16e51a364147b0a
braney
  Tue Jun 4 16:57:53 2019 -0700
look for BAM index by just adding .bai to the end of the bam file, and
if that does NOT work , try replacing the old suffix (presumably .bam)
with .bai and try that.   Also, we weren't adding the whole URL to
bigDataIndex in hubs, so now we do.

diff --git src/hg/lib/trackHub.c src/hg/lib/trackHub.c
index 71a28b4..60c0b6d 100644
--- src/hg/lib/trackHub.c
+++ src/hg/lib/trackHub.c
@@ -742,30 +742,31 @@
 {
 struct hashEl *hel = hashLookup(settingsHash, variable);
 if (hel != NULL)
     {
     char *oldVal = hel->val;
     hel->val = trackHubRelativeUrl(hubUrl, oldVal);
     freeMem(oldVal);
     }
 }
 
 static void expandBigDataUrl(struct trackHub *hub, struct trackHubGenome *genome,
 	struct trackDb *tdb)
 /* Expand bigDataUrls so that no longer relative to genome->trackDbFile */
 {
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "bigDataUrl");
+expandOneUrl(tdb->settingsHash, genome->trackDbFile, "bigDataIndex");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "frames");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "summary");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "linkDataUrl");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "searchTrix");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "barChartSampleUrl");
 expandOneUrl(tdb->settingsHash, genome->trackDbFile, "barChartMatrixUrl");
 }
 
 struct trackHubGenome *trackHubFindGenome(struct trackHub *hub, char *genomeName)
 /* Return trackHubGenome of given name associated with hub.  Return NULL if no
  * such genome. */
 {
 return hashFindVal(hub->genomeHash, genomeName);
 }