bfcefea92e26b0f5f5094607b071b6fa83ccf110
braney
  Tue Sep 16 16:15:38 2014 -0700
color mismatches as red ticks in mafs
diff --git src/hg/hgTracks/mafTrack.c src/hg/hgTracks/mafTrack.c
index 1fe1cec..d6adcaf 100644
--- src/hg/hgTracks/mafTrack.c
+++ src/hg/hgTracks/mafTrack.c
@@ -654,31 +654,33 @@
             for (i=0; i<w; ++i)
                 {
                 if (vis == tvFull)
                     {
                     int y = pixelScores[i] * height1;
                     hvGfxBox(hvg, i+x1, yOff + height1 - y, 
                         1, y+1, (ixMafAli % 2) ? color : altColor);
                     }
                 else
                     {
                     int shade = (pixelScores[i] * maxShade) + 1;
                     Color c;
                     if (shade > maxShade)
                         shade = maxShade;
                     c = shadesOfGray[shade];
-                    //hvGfxBox(hvg, i+x1, yOff+2, 1, height - 5, c);
+		    // draw mismatched bases as RED
+		    if (pixelScores[i] < 1.0)
+			c = MG_RED;
                     hvGfxBox(hvg, i+x1, yOff, 1, height - 1, c);
                     }
                 }
             if (vis != tvFull && mc->leftStatus == MAF_NEW_NESTED_STATUS)
 		{
 		hvGfxBox(hvg, x1-1, yOff, 2, 1, getChromBreakGreenColor());
 		hvGfxBox(hvg, x1-1, yOff, 1, height, getChromBreakGreenColor());
 		hvGfxBox(hvg, x1-1, yOff + height-1, 2, 1, 
                                 getChromBreakGreenColor());
 		}
             if (vis != tvFull && mc->rightStatus == MAF_NEW_NESTED_STATUS)
 		{
 		hvGfxBox(hvg, i+x1-1, yOff, 2, 1, getChromBreakGreenColor());
 		hvGfxBox(hvg, i+x1, yOff, 1, height, getChromBreakGreenColor());
 		hvGfxBox(hvg, i+x1-1, yOff + height-1, 2, 1,