ce941b2d389adadeb4955b5a7b2066d0dc7825a3
max
  Tue Oct 28 13:09:58 2014 -0700
adding a checkbox to bam track config to switch to bamWig mode
diff --git src/hg/hgTracks/bamTrack.c src/hg/hgTracks/bamTrack.c
index 83699e6..7d1bece 100644
--- src/hg/hgTracks/bamTrack.c
+++ src/hg/hgTracks/bamTrack.c
@@ -774,30 +774,38 @@
 if (!hashLookup(settings, INDEL_DOUBLE_INSERT))
     hashAdd(settings, INDEL_DOUBLE_INSERT, cloneString("on"));
 if (!hashLookup(settings, INDEL_QUERY_INSERT))
     hashAdd(settings, INDEL_QUERY_INSERT, cloneString("on"));
 if (!hashLookup(settings, INDEL_POLY_A))
     hashAdd(settings, INDEL_POLY_A, cloneString("on"));
 if (!hashLookup(settings, "showDiffBasesMaxZoom"))
     hashAdd(settings, "showDiffBasesMaxZoom", cloneString(BAM_DEFAULT_SHOW_DIFF_BASES_MAX_ZOOM));
 }
 
 void bamMethods(struct track *track)
 /* Methods for BAM alignment files. */
 {
 knetUdcInstall();
 
+boolean isBamWig = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
+			 BAMWIG_MODE, (trackDbSettingClosestToHome(track->tdb, BAMWIG_MODE) != NULL)); 
+if (isBamWig)
+    {
+    bamWigMethods(track, track->tdb, 0, NULL);
+    return;
+    }
+
 track->canPack = TRUE;
 boolean isPaired = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
 			 BAM_PAIR_ENDS_BY_NAME,
 			 (trackDbSettingClosestToHome(track->tdb, BAM_PAIR_ENDS_BY_NAME) != NULL));
 char *tdbShowNames = trackDbSetting(track->tdb, BAM_SHOW_NAMES);
 boolean showNames = cartUsualBooleanClosestToHome(cart, track->tdb, FALSE,
 						  BAM_SHOW_NAMES, SETTING_IS_ON(tdbShowNames));
 char *colorMode = cartOrTdbString(cart, track->tdb, BAM_COLOR_MODE, BAM_COLOR_MODE_DEFAULT);
 char *userTag = cartOrTdbString(cart, track->tdb, BAM_COLOR_TAG, BAM_COLOR_TAG_DEFAULT);
 if (sameString(colorMode, BAM_COLOR_MODE_TAG) && userTag != NULL)
     {
     if (! (isalpha(userTag[0]) && isalnum(userTag[1]) && userTag[2] == '\0'))
 	{
 	warn("%s: BAM tag '%s' is not valid -- must be a letter followed by a letter or number.",
 	     track->tdb->shortLabel, htmlEncode(userTag));