173bacbf6c28737266ef93048446902620b49330
braney
  Mon Dec 14 12:33:16 2015 -0800
some tweaks to CRAM support #14717

diff --git src/hg/hgTracks/bamTrack.c src/hg/hgTracks/bamTrack.c
index ff1ae25..a124a9e 100644
--- src/hg/hgTracks/bamTrack.c
+++ src/hg/hgTracks/bamTrack.c
@@ -487,30 +487,32 @@
 {
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     struct hash *pairHash = isPaired ? hashNew(18) : NULL;
     int minAliQual = atoi(cartOrTdbString(cart, tg->tdb, BAM_MIN_ALI_QUAL, BAM_MIN_ALI_QUAL_DEFAULT));
     char *colorMode = cartOrTdbString(cart, tg->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
     char *grayMode = cartOrTdbString(cart, tg->tdb, BAM_GRAY_MODE, BAM_GRAY_MODE_DEFAULT);
     char *userTag = cartOrTdbString(cart, tg->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
     int aliQualShadeMin = 0, aliQualShadeMax = 99, baseQualShadeMin = 0, baseQualShadeMax = 40;
     parseIntRangeSetting(tg->tdb, "aliQualRange", &aliQualShadeMin, &aliQualShadeMax);
     parseIntRangeSetting(tg->tdb, "baseQualRange", &baseQualShadeMin, &baseQualShadeMax);
     struct bamTrackData btd = {tg, pairHash, minAliQual, colorMode, grayMode, userTag,
 			       aliQualShadeMin, aliQualShadeMax, baseQualShadeMin, baseQualShadeMax};
+    cramInit(tg->tdb);
+
     char *fileName = trackDbSetting(tg->tdb, "bigDataUrl");
     if (fileName == NULL)
 	{
 	if (tg->customPt)
 	    {
 	    errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->track);
 	    }
 	else
 	    {
 	    struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb);
 	    fileName = bamFileNameFromTable(conn, tg->table, chromName);
 	    hFreeConn(&conn);
 	    }
 	}