0d3b8feb6074f6caccc2d4aadd020961fbd7eb82
chmalee
  Wed Jun 10 14:39:38 2020 -0700
Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582

diff --git src/hg/inc/vcfUi.h src/hg/inc/vcfUi.h
index af8b34a..c480b0d 100644
--- src/hg/inc/vcfUi.h
+++ src/hg/inc/vcfUi.h
@@ -41,32 +41,33 @@
 
 #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"
+#define VCF_PHASED_CHILD_BELOW_VAR "sortChildBelow"
 
 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);
+struct slPair *vcfPhasedGetSampleOrder(struct cart *cart, struct trackDb *tdb, boolean parentLevel, boolean hideOtherSamples);
 /* 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