936b5b5319541bf59421b258703a4f6af54790e3
tdreszer
  Wed Jul 30 08:45:57 2014 -0700
Two problems noticed by Angie in code review.  Redmine #13704.
diff --git src/hg/hgTracks/bamTrack.c src/hg/hgTracks/bamTrack.c
index b6ecf69..3f2c2c4 100644
--- src/hg/hgTracks/bamTrack.c
+++ src/hg/hgTracks/bamTrack.c
@@ -594,30 +594,31 @@
 
 static Color darkBlueColor = 0;
 static Color darkRedColor = 0;
 if (darkRedColor == 0)
     {
     darkRedColor = hvGfxFindColorIx(hvg, 100,0,0);
     darkBlueColor = hvGfxFindColorIx(hvg, 0,0,100);
     }
 if (sameString(colorMode, BAM_COLOR_MODE_STRAND))
     color = (lf->orientation < 0) ? darkRedColor : darkBlueColor;
 else if (lf->filterColor != 0)
     {
     // In bamTrack, lf->filterColor is an RGBA value
     color = lf->filterColor;
     }
+else
     color = colorBySpectrumOrDefault(hvg,tg,lf->grayIx,tg->ixColor);
 
 indelEnabled(cart, tg->tdb, basesPerPixel, &indelShowDoubleInsert, &indelShowQueryInsert,
 	     &indelShowPolyA);
 if (!indelShowDoubleInsert)
     innerLine(hvg, x1, midY, w, color);
 for (sf = lf->components; sf != NULL; sf = sf->next)
     {
     int s = sf->start,  e = sf->end;
     if (e <= s || e < winStart || s > winEnd)
 	continue;
     if (baseQualMode)
         color = colorBySpectrumOrDefault(hvg,tg,sf->grayIx,color);
     baseColorDrawItem(tg, lf, sf->grayIx, hvg, xOff, y, scale, font, s, e, heightPer,
 		      zoomedToCodonLevel, mrnaSeq, sf, psl, drawOpt, MAXPIXELS, winStart, color);