e8405a958dae40b261b2eadcd59a20edc64761f1
angie
  Wed May 13 15:25:04 2020 -0700
VCF details and track controls: use "sample" instead of "haplotype" when displaying SARS-CoV-2 data because viruses are not diploid.  refs #25409
Also don't display "leaf cluster" shape option, which applies only to the center-weighted haplotype clustering, unless that method is selected.

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index 8fac5e0..84f0848 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -1,56 +1,59 @@
 /* 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_METHOD_VAR "hapClusterMethod"
 #define VCF_HAP_METHOD_CENTER_WEIGHTED "centerWeighted"
 #define VCF_HAP_METHOD_FILE_ORDER "fileOrder"
 #define VCF_HAP_METHOD_TREE_FILE "treeFile"
 #define VCF_DEFAULT_HAP_METHOD VCF_HAP_METHOD_CENTER_WEIGHTED
 
 #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. */
 
+char *vcfHaplotypeOrSample(struct cart *cart);
+/* Return "Sample" if the current organism is uniploid (like SARS-CoV-2), "Haplotype" otherwise. */
+
 #endif//def VCF_UI