6c3d002050d3381a545c4d561f3fc147ba7c886f
braney
  Wed Jan 15 15:18:55 2014 -0800
draw the pale yellow for N's in snakes
diff --git src/hg/hgTracks/snakeTrack.c src/hg/hgTracks/snakeTrack.c
index 452790e..5f69ab7 100644
--- src/hg/hgTracks/snakeTrack.c
+++ src/hg/hgTracks/snakeTrack.c
@@ -794,31 +794,34 @@
 	    }
 	int si = s;
 	char *ptr1 = refDna;
 	char *ptr2 = ourDna;
 	for(; si < e; si++,ptr1++,ptr2++)
 	    {
 	    if (*ptr1 != *ptr2)
 		{
 		int misX1 = round((double)((int)si-winStart)*scale) + xOff;
 		int misX2 = round((double)((int)(si+1)-winStart)*scale) + xOff;
 		int w1 = misX2 - misX1;
 		if (w1 < 1)
 		    w1 = 1;
 
 		// mismatch!
-		hvGfxBox(hvg, misX1, y, w1, heightPer, MG_RED);
+		Color boxColor = MG_RED;
+		if ((*ptr2 == 'N') || (*ptr2 == 'n'))
+		    boxColor = hvGfxFindRgb(hvg, &undefinedYellowColor);
+		hvGfxBox(hvg, misX1, y, w1, heightPer, boxColor);
 		}
 	    }
 
 	// if we're zoomed to base level, draw sequence of mismatch
 	if (zoomedToBaseLevel)
 	    {
 	    int mysx = round((double)((int)s-winStart)*scale) + xOff;
 	    int myex = round((double)((int)e-winStart)*scale) + xOff;
 	    int myw = myex - mysx;
 	    spreadAlignString(hvg, mysx, y, myw, heightPer, MG_WHITE, font, ourDna,
 		refDna, seqLen, TRUE, FALSE);
 	    }
 
     }
     sf->drawn = TRUE;