a61d43c445b0e9ead7e956bef4efc1f983d75c3d
angie
  Wed Aug 7 07:41:32 2013 -0700
For BAM custom tracks, base-coloring trackDb settings were automatically set,but that didn't take care of hub tracks, and not all native BAM tracks added
those settings in their trackDb entries.  So, as I should have done from the
beginning, I'm forcing the base-coloring settings directly in bamMethods.
fixes #11479

diff --git src/hg/hgTracks/hgTracks.c src/hg/hgTracks/hgTracks.c
index 35c970d..b0692b9 100644
--- src/hg/hgTracks/hgTracks.c
+++ src/hg/hgTracks/hgTracks.c
@@ -3219,37 +3219,30 @@
 else if (sameString(type, "encodePeak"))
     {
     tg = trackFromTrackDb(tdb);
     encodePeakMethodsCt(tg);
     tg->nextItemButtonable = TRUE;
     tg->customPt = ct;
     }
 else if (sameString(type, "bam"))
     {
     tg = trackFromTrackDb(tdb);
     tg->customPt = ct;
     bamMethods(tg);
     if (trackShouldUseAjaxRetrieval(tg))
         tg->loadItems = dontLoadItems;
     tg->mapItemName = ctMapItemName;
-    hashAdd(tdb->settingsHash, BASE_COLOR_USE_SEQUENCE, cloneString("lfExtra"));
-    hashAdd(tdb->settingsHash, BASE_COLOR_DEFAULT, cloneString("diffBases"));
-    hashAdd(tdb->settingsHash, SHOW_DIFF_BASES_ALL_SCALES, cloneString("."));
-    hashAdd(tdb->settingsHash, INDEL_DOUBLE_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_QUERY_INSERT, cloneString("on"));
-    hashAdd(tdb->settingsHash, INDEL_POLY_A, cloneString("on"));
-    hashAdd(tdb->settingsHash, "showDiffBasesMaxZoom", cloneString("100"));
     }
 else if (sameString(type, "vcfTabix"))
     {
     tg = trackFromTrackDb(tdb);
     tg->customPt = ct;
     vcfTabixMethods(tg);
     if (trackShouldUseAjaxRetrieval(tg))
         tg->loadItems = dontLoadItems;
     tg->mapItemName = ctMapItemName;
     }
 else if (sameString(type, "makeItems"))
     {
     tg = trackFromTrackDb(tdb);
     makeItemsMethods(tg);
     tg->nextItemButtonable = TRUE;