e46073f856770bdfef4f7637eea8f9f9297aa139
chmalee
  Tue Nov 19 15:57:08 2019 -0800
Initial commit of new track type vcfPhased trio. A line with ticks, one
per haplotype per sample in the VCF, as specified by trackDb variables.

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index 84f0848..d7efa67 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -32,28 +32,39 @@
 #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
 
+#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"
+
 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);
+/* 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. */
 
 #endif//def VCF_UI