d27baba8d7c7c0e779a3d79cb6d17b97055c40bc
angie
  Mon Jul 28 16:42:58 2014 -0700
David pointed out that it is inappropriate to show Hardy-Weinberg equilibriumfrequencies on the VCF details page unless the VCF data are from a population
study -- so at this point, pretty much only 1000 Genomes.  So I added a new
trackDb setting for vcf/vcfTabix, showHardyWeinberg, and added it to the
1000 Genomes track def.

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index 1847f20..053de6e 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -1,49 +1,51 @@
 /* vcfUi - Variant Call Format user interface controls that are shared
  * between more than one CGI. */
 
 /* Copyright (C) 2011 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 #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_SHOW_HW_VAR "showHardyWeinberg"
+
 #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 parentLevel, 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