42ac1b41b5b3b66ed8ea7828cd36f4fcd9ceb1d5
braney
  Thu Sep 27 14:38:17 2018 -0700
fix bug in gencode knownGene bigBed support #22145

diff --git src/hg/hgTracks/simpleTracks.c src/hg/hgTracks/simpleTracks.c
index 73de7e0..1f8d85a 100644
--- src/hg/hgTracks/simpleTracks.c
+++ src/hg/hgTracks/simpleTracks.c
@@ -6303,31 +6303,31 @@
 struct linkedFeatures *lf = lfList;
 for(;lf;lf = lf->next)
     lf->isBigGenePred = TRUE;
 struct linkedFeatures *newList = lfList;
 
 if (isGencode)
     {
     char varName[SMALLBUF];
     safef(varName, sizeof(varName), "%s.show.comprehensive", tg->tdb->track);
     boolean showComprehensive = cartUsualBoolean(cart, varName, FALSE);
     if (!showComprehensive)
         newList = stripLinkedFeaturesWithoutBitInScore(lfList,  BIT_BASIC);
     safef(varName, sizeof(varName), "%s.show.pseudo", tg->tdb->track);
     boolean showPseudo = cartUsualBoolean(cart, varName, FALSE);
     if (!showPseudo)
-        newList = stripLinkedFeaturesWithBitInScore(lfList,  BIT_PSEUDO);
+        newList = stripLinkedFeaturesWithBitInScore(newList,  BIT_PSEUDO);
     }
 
 slSort(&newList, linkedFeaturesCmp);
 tg->items = newList;
 tg->itemColor   = bigGenePredColor;
 tg->itemNameColor = bigGenePredColor;
 }
 
 void loadKnownGene(struct track *tg)
 /* Load up known genes. */
 {
 struct trackDb *tdb = tg->tdb;
 boolean isGencode = trackDbSettingOn(tdb, "isGencode") || trackDbSettingOn(tdb, "isGencode2");
 char *bigGenePred = trackDbSetting(tdb, "bigGeneDataUrl");
 struct udcFile *file;