298302978224472f8e84720e6c11272684346e6b
braney
  Wed Apr 22 12:24:25 2020 -0700
add some code to recognize ribosomal slips in codon display mode.  Only
works on the + stand right now for wuhCor1

diff --git src/hg/hgTracks/cds.h src/hg/hgTracks/cds.h
index ea6403d..4d09f08 100644
--- src/hg/hgTracks/cds.h
+++ src/hg/hgTracks/cds.h
@@ -73,31 +73,42 @@
 #define CDS_ALT_START    10
 #define CDS_ALT_START_R  0 
 #define CDS_ALT_START_G  0 
 #define CDS_ALT_START_B  128
 
 #define CDS_SYN_PROT    11   /* yellow, protein seq change "synonymous" ie I->V , R->K etc */
 #define CDS_SYN_PROT_R  255 
 #define CDS_SYN_PROT_G  215 
 #define CDS_SYN_PROT_B  0
 
 #define CDS_SYN_BLEND    12  /* brown, protein seq part syn and part non-syn */
 #define CDS_SYN_BLEND_R  100 
 #define CDS_SYN_BLEND_G  50 
 #define CDS_SYN_BLEND_B  0
 
-#define CDS_NUM_COLORS 13
+// Ribosomal shift colors
+#define CDS_RIBO_SLIP1    13  /* purple */
+#define CDS_RIBO_SLIP1_R  250 
+#define CDS_RIBO_SLIP1_G  50 
+#define CDS_RIBO_SLIP1_B  255
+
+#define CDS_RIBO_SLIP2    14  /* cyan */
+#define CDS_RIBO_SLIP2_R  50 
+#define CDS_RIBO_SLIP2_G  250 
+#define CDS_RIBO_SLIP2_B  255
+
+#define CDS_NUM_COLORS 15
 
 Color getCdsColor(int index);
 /* return color from index of types of colors */
 
 enum baseColorDrawOpt baseColorGetDrawOpt(struct track *tg);
 /* Determine what base/codon coloring option (if any) has been selected 
  * in trackDb/cart, and gate with zoom level. */
 
 
 struct simpleFeature *baseColorCodonsFromGenePred(struct linkedFeatures *lf,
         struct genePred *gp, boolean colorStopStart, boolean codonNumbering);
 /* Given an lf and the genePred from which the lf was constructed, 
  * return a list of simpleFeature elements, one per codon (or partial 
  * codon if the codon falls on a gap boundary. */