bd53b8dfe0a86f9d1c8ed57289fd409a6c52bd6b
chmalee
  Fri Jun 26 10:54:41 2020 -0700
Add option to shade alleles by inconsitent transmission between child
and parent haplotypes

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index 31fa100..af8b34a 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -40,30 +40,31 @@
 #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
 
 #define VCF_PHASED_CHILD_SAMPLE_SETTING "vcfChildSample"
 #define VCF_PHASED_PARENTS_SAMPLE_SETTING "vcfParentSamples"
 #define VCF_PHASED_SAMPLE_ORDER_VAR "vcfSampleOrder"
 #define VCF_PHASED_MAX_OTHER_SAMPLES 2
 #define VCF_PHASED_DEFAULT_LABEL_VAR "doDefaultLabel"
 #define VCF_PHASED_ALIAS_LABEL_VAR "doAliasLabel"
 #define VCF_PHASED_HIDE_OTHER_VAR "hideParents"
 #define VCF_PHASED_TDB_USE_ALT_NAMES "vcfUseAltSampleNames"
+#define VCF_PHASED_HIGHLIGHT_INCONSISTENT "vcfHighlightDiffs"
 
 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. */
 
 struct slPair *vcfPhasedGetSampleOrder(struct cart *cart, struct trackDb *tdb, boolean parentLevel);
 /* Parse out a trio sample order from trackDb */
 
 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. */