791097ea7589f6fadcf825c5c3a8934054917a28
angie
  Thu Jul 9 14:38:12 2020 -0700
VCF haplotype display: trackDb setting geneTrack adds option to color by function (red for non-synon, green for synon, blue for UTR/NC).  refs #25870

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 8702fd6..52a7e2f 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -249,30 +249,41 @@
 safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name);
 cgiMakeCheckBox(cartVar, hapClustEnabled);
 printf("<B>Enable %s sorting display</B><BR>\n", vcfHaplotypeOrSample(cart));
 }
 
 static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean parentLevel)
 /* Let the user choose how to color the sorted haplotypes. */
 {
 printf("<B>Allele coloring scheme:</B><BR>\n");
 char *colorBy = cartOrTdbString(cart, tdb, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_ALTONLY, sameString(colorBy, VCF_HAP_COLORBY_ALTONLY));
 printf("reference alleles invisible, alternate alleles in black<BR>\n");
+char *geneTrack = cartOrTdbString(cart, tdb, "geneTrack", NULL);
+if (isNotEmpty(geneTrack))
+    {
+    cgiMakeRadioButton(varName, VCF_HAP_COLORBY_FUNCTION,
+                       sameString(colorBy, VCF_HAP_COLORBY_FUNCTION));
+    printf("reference alleles invisible, alternate alleles in "
+           "<span style='color:red'>red</span> for non-synonymous, "
+           "<span style='color:green'>green</span> for synonymous, "
+           "<span style='color:blue'>blue</span> for UTR/noncoding, "
+           "black otherwise<BR>\n");
+    }
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT));
 printf("reference alleles in blue, alternate alleles in red<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, sameString(colorBy, VCF_HAP_COLORBY_BASE));
 printf("first base of allele (A = red, C = blue, G = green, T = magenta)<BR>\n");
 }
 
 static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean parentLevel)
 /* Let the user choose branch shape. */
 {
 // This option applies only to center-weighted clustering; don't show option when some other
 // method is selected.
 char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD);
 printf("<div id='leafShapeContainer'%s>\n",
        differentString(hapMethod, VCF_HAP_METHOD_CENTER_WEIGHTED) ? " style='display: none;'" : "");