2e5a07597bfa95dedb669fef2a5e2b8048f2c644
angie
  Mon Dec 5 08:08:23 2011 -0800
Feature #3711 (VCF haplo-sorting display): Implemented Richard Durbin'ssuggestions as new defaults:

1. Instead of ref=blue, alt=red, simply ignore ref and draw only alt, in black.
Draw top & bottom bounds of variants in extra pixel rows.

2. Draw the tree using open triangles instead of open rectangles.

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index ecc605e..d2a2b69 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -1,39 +1,46 @@
 /* vcfUi - Variant Call Format user interface controls that are shared
  * between more than one CGI. */
 #ifndef VCFUI_H
 #define VCFUI_H
 
 #include "cart.h"
 #include "trackDb.h"
 #include "vcf.h"
 
 #define VCF_HAP_HEIGHT_VAR "hapClusterHeight"
 #define VCF_DEFAULT_HAP_HEIGHT 128
 
 #define VCF_HAP_ENABLED_VAR "hapClusterEnabled"
 
 #define VCF_HAP_COLORBY_VAR "hapClusterColorBy"
+#define VCF_HAP_COLORBY_ALTONLY "altOnly"
 #define VCF_HAP_COLORBY_REFALT "refAlt"
 #define VCF_HAP_COLORBY_BASE "base"
+#define VCF_DEFAULT_HAP_COLORBY VCF_HAP_COLORBY_ALTONLY
+
+#define VCF_HAP_TREEANGLE_VAR "hapClusterTreeAngle"
+#define VCF_HAP_TREEANGLE_TRIANGLE "triangle"
+#define VCF_HAP_TREEANGLE_RECTANGLE "rectangle"
+#define VCF_DEFAULT_HAP_TREEANGLE VCF_HAP_TREEANGLE_TRIANGLE
 
 #define VCF_APPLY_MIN_QUAL_VAR "applyMinQual"
 #define VCF_DEFAULT_APPLY_MIN_QUAL FALSE
 
 #define VCF_MIN_QUAL_VAR "minQual"
 #define VCF_DEFAULT_MIN_QUAL 0
 
 #define VCF_EXCLUDE_FILTER_VAR "excludeFilterValues"
 
 #define VCF_MIN_ALLELE_FREQ_VAR "minFreq"
 #define VCF_DEFAULT_MIN_ALLELE_FREQ 0.0
 
 void vcfCfgHaplotypeCenter(struct cart *cart, struct trackDb *tdb, char *track,
 			   boolean compositeLevel, struct vcfFile *vcff,
 			   char *thisName, char *thisChrom, int thisPos, char *formName);
 /* If vcff has genotype data, show status and controls for choosing the center variant
  * for haplotype clustering/sorting in hgTracks. */
 
 void vcfCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed);
 /* Complete track controls for VCF. */
 
 #endif//def VCF_UI