60fe7778fc4b3cff11906e688a4e0e99aba43e9c
angie
  Mon Aug 30 21:03:08 2010 -0700
Fix to addBamPaired for code that detects unpaired items for gray mode -- Brian found that it was missing most of them, doh!
diff --git src/hg/hgTracks/bamTrack.c src/hg/hgTracks/bamTrack.c
index 841c2ba..db46891 100644
--- src/hg/hgTracks/bamTrack.c
+++ src/hg/hgTracks/bamTrack.c
@@ -340,6 +340,10 @@
     {
     if (lf->start < winEnd && lf->end > winStart)
 	slAddHead(&(tg->items), lfsFromLf(lf));
+    if ((core->flag & BAM_FMUNMAP) && sameString(btd->colorMode, BAM_COLOR_MODE_GRAY) &&
+	sameString(btd->grayMode, BAM_GRAY_MODE_UNPAIRED))
+	// not properly paired: make it a lighter shade.
+	lf->grayIx -= 4;
     }
 else
     {