ffbb6c9d2c322f07e7e8d206af3fa984b636906d
max
  Thu Jun 20 04:43:25 2024 -0700
always switch on itemRgb by default if alwaysItemRgb is on in hg.conf, refs #28498

diff --git src/hg/hgTracks/bedTrack.c src/hg/hgTracks/bedTrack.c
index 8127170..998762b 100644
--- src/hg/hgTracks/bedTrack.c
+++ src/hg/hgTracks/bedTrack.c
@@ -6,30 +6,31 @@
 #include "common.h"
 #include "jksql.h"
 #include "bed.h"
 #include "hdb.h"
 #include "bedCart.h"
 #include "bbiFile.h"
 #include "bigBed.h"
 #include "hgTracks.h"
 #include "cds.h"
 #include "bedTabix.h"
 #include "obscure.h"
 #include "bigBedFilter.h"
 #include "bigBedLabel.h"
 #include "snake.h"
 #include "quickLift.h"
+#include "hgConfig.h"
 
 #define SEQ_DELIM '~'
 
 struct bed *bedLoadPairedTagAlign(char **row)
 /* Load first six fields of bed.
  * Add ~seq1~seq2 to end of name
  * Then remove the sequence to extra field when we convert to linkedFeature.
  * Assumes seq1 and seq2 are in row[6] and row[7], as they would be with a
  * pairedTagAlign type (hg/lib/encode/pairedTagAlign.as). It would be good to be
  * able to check these columns exist but we dont have the sqlResult here. */
 {
 char buf[1024];
 struct bed *ret = bedLoad6(row);
 safef(buf, sizeof(buf), "%s%c%s%c%s", ret->name, SEQ_DELIM, row[6], SEQ_DELIM, row[7]);
 freez(&(ret->name));
@@ -226,31 +227,31 @@
 if ((bed->thickEnd != 0) &&
     ((bed->thickEnd < bed->chromStart) ||
      (bed->thickEnd > bed->chromEnd)))
     bed->thickEnd = bed->chromEnd;
 }
 
 struct linkedFeatures *bedMungToLinkedFeatures(struct bed **pBed, struct trackDb *tdb,
 	int fieldCount, int scoreMin, int scoreMax, boolean useItemRgb)
 /* Convert bed to a linkedFeature, destroying bed in the process. */
 {
 struct bed *bed = *pBed;
 if (fieldCount < 12)
     bed8To12(bed);
 adjustBedScoreGrayLevel(tdb, bed, scoreMin, scoreMax);
 struct linkedFeatures *lf = lfFromBedExtra(bed, scoreMin, scoreMax);
-if (useItemRgb)
+if (useItemRgb || (fieldCount > 8 && cfgOptionBooleanDefault("alwaysItemRgb", TRUE)))
     {
     lf->useItemRgb = TRUE;
     lf->filterColor=bed->itemRgb;
     }
 bedFree(pBed);
 return lf;
 }
 
 void loadBed9(struct track *tg)
 /* Convert bed 9 info in window to linked feature.  (to handle itemRgb)*/
 {
 struct trackDb *tdb = tg->tdb;
 struct bed *bed;
 struct linkedFeatures *lfList = NULL, *lf;
 int scoreMin = atoi(trackDbSettingClosestToHomeOrDefault(tdb, "scoreMin", "0"));