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/lib/vcfUi.c src/hg/lib/vcfUi.c
index 045f92c..4847cfa 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -1,425 +1,536 @@
 /* vcfUi - Variant Call Format user interface controls that are shared
  * between more than one CGI. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
 #include "common.h"
 #include "cheapcgi.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "hui.h"
 #include "jsHelper.h"
 #include "vcf.h"
 #include "vcfUi.h"
 #include "knetUdc.h"
 #include "udc.h"
 
 INLINE char *nameOrDefault(char *thisName, char *defaultVal)
 /* If thisName is not a placeholder value, return it; otherwise return default. */
 {
 if (isNotEmpty(thisName) && !sameString(thisName, "."))
     return thisName;
 return defaultVal;
 }
 
 #define VCF_HAPLOSORT_DEFAULT_DESC "middle variant in viewing window"
 
 static void vcfCfgHaplotypeCenterHiddens(char *track, char *ctrName, char *ctrChrom, int ctrPos)
 /* Make hidden form inputs and button for setting the center variant for haplotype
  * clustering/sorting in hgTracks. */
 {
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s.centerVariantChrom", track);
 cgiMakeHiddenVar(cartVar, ctrChrom);
 safef(cartVar, sizeof(cartVar), "%s.centerVariantPos", track);
 char ctrPosStr[16];
 safef(ctrPosStr, sizeof(ctrPosStr), "%d", ctrPos);
 cgiMakeHiddenVar(cartVar, ctrPosStr);
 safef(cartVar, sizeof(cartVar), "%s.centerVariantName", track);
 cgiMakeHiddenVar(cartVar, ctrName);
 }
 
 char *vcfHaplotypeOrSample(struct cart *cart)
 /* Return "Sample" if the current organism is uniploid (like SARS-CoV-2), "Haplotype" otherwise. */
 {
 // We should make a better way of determining whether the organism is diploid,
 // but for now this will prevent David from being bothered by diploid terminology
 // when viewing SARS-CoV-2 variants:
 return sameOk(cartOptionalString(cart, "db"), "wuhCor1") ? "Sample" : "Haplotype";
 }
 
 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. */
 {
 if (vcff != NULL && vcff->genotypeCount > 1)
     {
     printf("using ");
     char *centerChrom = cartOptionalStringClosestToHome(cart, tdb, parentLevel,
 							"centerVariantChrom");
     if (isEmpty(centerChrom))
 	{
 	// Unspecified in cart -- describe the default action
 	printf(VCF_HAPLOSORT_DEFAULT_DESC " as anchor.</TD></TR>\n");
 	if (isNotEmpty(thisChrom))
 	    {
 	    // but we do have a candidate, so offer to make it the center:
 	    puts("<TR><TD></TD><TD>");
 	    vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos);
 	    char label[256];
 	    safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant"));
 	    cgiMakeButton("setCenterSubmit", label);
 	    printf(" as anchor</TD></TR>\n");
 	    }
 	else
             {
 	    printf("<TR><TD></TD><TD>");
             char *hapOrSample = vcfHaplotypeOrSample(cart);
             if (sameString(hapOrSample, "Sample"))
                 {
                 puts("Samples are clustered by similarity around a central variant. "
                      "Samples are reordered for display using the clustering tree, which is "
                      "drawn in the left label area.");
                 }
             else
                 {
                 puts("If this mode is selected and genotypes are phased or homozygous, "
                      "then each genotype is split into two independent haplotypes. "
                      "These local haplotypes are clustered by similarity around a central variant. "
                      "Haplotypes are reordered for display using the clustering tree, which is "
                      "drawn in the left label area. "
                      "Local haplotype blocks can often be identified using this display.");
                 }
             printf("<br>To anchor the sorting to a particular variant, "
 		   "click on the variant in the genome browser, "
 		   "and then click on the 'Use this variant' button on the next page."
 		   "</TD></TR>\n");
             }
 	}
     else
 	{
 	// Describe the one specified in cart.
 	int centerPos = cartUsualIntClosestToHome(cart, tdb, parentLevel, "centerVariantPos",
 						  -1);
 	char *centerName = cartStringClosestToHome(cart, tdb, parentLevel, "centerVariantName");
 	if (isNotEmpty(thisChrom))
 	    {
 	    // These form inputs are for either "use me" or clear:
 	    vcfCfgHaplotypeCenterHiddens(track, thisName, thisChrom, thisPos);
 	    // Is this variant the same as the center variant specified in cart?
 	    if (sameString(thisChrom, centerChrom) && sameString(thisName, centerName) &&
 		thisPos == centerPos)
 		printf("this variant as anchor.</TD></TR>\n");
 	    else
 		{
 		// make a "use me" button
 		printf("%s at %s:%d as anchor.</TD></TR>\n<TR><TD></TD><TD>\n",
 		       nameOrDefault(centerName, "variant"), centerChrom, centerPos+1);
 		char label[256];
 		safef(label, sizeof(label), "Use %s", nameOrDefault(thisName, "this variant"));
 		cgiMakeButton("replaceCenterSubmit", label);
 		printf(" as anchor</TD></TR>\n");
 		}
 	    }
 	else
 	    {
 	    // Form inputs (in case the clear button is clicked)
 	    vcfCfgHaplotypeCenterHiddens(track, centerName, centerChrom, centerPos);
 	    printf("%s at %s:%d as anchor.</TD></TR>\n",
 		   nameOrDefault(centerName, "variant"), centerChrom, centerPos+1);
 	    }
 	// Make a clear button that modifies the hiddens using onClick
 	puts("<TR><TD></TD><TD>");
 	struct dyString *onClick = dyStringNew(0);
 	dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantChrom', ''); ",
 		       formName, track);
 	dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantName', ''); ",
 		       formName, track);
 	dyStringPrintf(onClick, "updateOrMakeNamedVariable(%s, '%s.centerVariantPos', 0);",
 		       formName, track);
 	dyStringPrintf(onClick, "document.%s.submit(); return false;", formName);
 	cgiMakeButtonWithOnClick("clearCenterSubmit", "Clear selection", NULL, onClick->string);
 	printf(" (use " VCF_HAPLOSORT_DEFAULT_DESC ")</TD></TR>\n");
 	}
     }
 }
 
 static void vcfCfgHaplotypeMethod(struct cart *cart, struct trackDb *tdb, char *track,
                                   boolean parentLevel, struct vcfFile *vcff)
 /* If vcff has genotype data, offer the option of whether to cluster or just use the order
  * of genotypes in the VCF file.  For clustering, show status and controls for choosing the
  * center variant for haplotype clustering/sorting in hgTracks. */
 {
 if (vcff != NULL && vcff->genotypeCount > 1)
     {
     printf("<TABLE cellpadding=0><TR><TD colspan=2>"
 	   "<B>%s sorting order:</B></TD></TR>\n", vcfHaplotypeOrSample(cart));
     // If trackDb specifies a treeFile, offer that as an option
     char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD);
     char *hapMethodTdb = trackDbSetting(tdb, VCF_HAP_METHOD_VAR);
     char varName[1024];
     safef(varName, sizeof(varName), "%s." VCF_HAP_METHOD_VAR, track);
     if (hapMethodTdb && startsWithWord("treeFile", hapMethodTdb))
         {
         puts("<TR><TD>");
         cgiMakeRadioButton(varName, VCF_HAP_METHOD_TREE_FILE,
                            startsWithWord(VCF_HAP_METHOD_TREE_FILE, hapMethod));
         printf("</TD><TD>using the tree specified in file associated with track</TD></TR>");
         }
     printf("<TR><TD>");
     cgiMakeRadioButton(varName, VCF_HAP_METHOD_CENTER_WEIGHTED,
                        sameString(hapMethod, VCF_HAP_METHOD_CENTER_WEIGHTED));
     printf("</TD><TD>");
     vcfCfgHaplotypeCenter(cart, tdb, track, parentLevel, vcff, NULL, NULL, 0, "mainForm");
     puts("<TR><TD>");
     cgiMakeRadioButton(varName, VCF_HAP_METHOD_FILE_ORDER,
                        sameString(hapMethod, VCF_HAP_METHOD_FILE_ORDER));
     puts("</TD><TD>using the order in which samples appear in the underlying VCF file</TD></TR>");
     puts("</TABLE>");
     jsInlineF("$('input[type=radio][name=\"%s\"]').change(function() { "
               "if (this.value == '"VCF_HAP_METHOD_CENTER_WEIGHTED"') {"
               "  $('#leafShapeContainer').show();"
               "} else {"
               "  $('#leafShapeContainer').hide();"
               "}});\n",
               varName);
     }
 }
 
 //TODO: share this code w/hgTracks, hgc in hg/lib/vcfFile.c
 static struct vcfFile *vcfHopefullyOpenHeader(struct cart *cart, struct trackDb *tdb)
 /* Defend against network errors and return the vcfFile object with header data, or NULL. */
 {
 knetUdcInstall();
 if (udcCacheTimeout() < 300)
     udcSetCacheTimeout(300);
 char *fileOrUrl = trackDbSetting(tdb, "bigDataUrl");
 if (isEmpty(fileOrUrl))
     {
     char *db = cartString(cart, "db");
     char *table = tdb->table;
     char *dbTableName = trackDbSetting(tdb, "dbTableName");
     struct sqlConnection *conn;
     if (isCustomTrack(tdb->track) && isNotEmpty(dbTableName))
         {
         conn =  hAllocConn(CUSTOM_TRASH);
         table = dbTableName;
         }
     else
         conn = hAllocConnTrack(db, tdb);
     char *chrom = cartOptionalString(cart, "c");
     if (chrom != NULL)
         fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, chrom);
     if (fileOrUrl == NULL)
         fileOrUrl = bbiNameFromSettingOrTableChrom(tdb, conn, table, hDefaultChrom(db));
     hFreeConn(&conn);
     }
 if (fileOrUrl == NULL)
     return NULL;
 int vcfMaxErr = 100;
 struct vcfFile *vcff = NULL;
 /* protect against temporary network error */
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     if (startsWithWord("vcfTabix", tdb->type))
 	vcff = vcfTabixFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr, -1);
     else
 	vcff = vcfFileMayOpen(fileOrUrl, NULL, 0, 0, vcfMaxErr, -1, FALSE);
     }
 errCatchEnd(errCatch);
 if (errCatch->gotError)
     {
     if (isNotEmpty(errCatch->message->string))
 	warn("unable to open %s: %s", fileOrUrl, errCatch->message->string);
     }
 errCatchFree(&errCatch);
 return vcff;
 }
 
 static void vcfCfgHapClusterEnable(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean parentLevel)
 /* Let the user enable/disable haplotype sorting display. */
 {
 boolean hapClustEnabled = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE);
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name);
 cgiMakeCheckBox(cartVar, hapClustEnabled);
 printf("<B>Enable %s sorting display</B><BR>\n", vcfHaplotypeOrSample(cart));
 }
 
 static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean parentLevel)
 /* Let the user choose how to color the sorted haplotypes. */
 {
 printf("<B>Allele coloring scheme:</B><BR>\n");
 char *colorBy = cartOrTdbString(cart, tdb, VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_ALTONLY, sameString(colorBy, VCF_HAP_COLORBY_ALTONLY));
 printf("reference alleles invisible, alternate alleles in black<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, sameString(colorBy, VCF_HAP_COLORBY_REFALT));
 printf("reference alleles in blue, alternate alleles in red<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_BASE, sameString(colorBy, VCF_HAP_COLORBY_BASE));
 printf("first base of allele (A = red, C = blue, G = green, T = magenta)<BR>\n");
 }
 
 static void vcfCfgHapClusterTreeAngle(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean parentLevel)
 /* Let the user choose branch shape. */
 {
 // This option applies only to center-weighted clustering; don't show option when some other
 // method is selected.
 char *hapMethod = cartOrTdbString(cart, tdb, VCF_HAP_METHOD_VAR, VCF_DEFAULT_HAP_METHOD);
 printf("<div id='leafShapeContainer'%s>\n",
        differentString(hapMethod, VCF_HAP_METHOD_CENTER_WEIGHTED) ? " style='display: none;'" : "");
 printf("<B>%s clustering tree leaf shape:</B><BR>\n", vcfHaplotypeOrSample(cart));
 char *treeAngle = cartOrTdbString(cart, tdb, VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_TREEANGLE_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_TRIANGLE,
 		   sameString(treeAngle, VCF_HAP_TREEANGLE_TRIANGLE));
 printf("draw branches whose samples are all identical as &lt;<BR>\n");
 cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE,
 		   sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE));
 printf("draw branches whose samples are all identical as [<BR>\n");
 puts("</div>");
 }
 
 static void vcfCfgHapClusterHeight(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 				   char *name, boolean parentLevel)
 /* Let the user specify a height for the track. */
 {
 if (vcff != NULL && vcff->genotypeCount > 1)
     {
     printf("<B>%s sorting display height:</B> \n", vcfHaplotypeOrSample(cart));
     int cartHeight = cartOrTdbInt(cart, tdb, VCF_HAP_HEIGHT_VAR, VCF_DEFAULT_HAP_HEIGHT);
     char varName[1024];
     safef(varName, sizeof(varName), "%s." VCF_HAP_HEIGHT_VAR, name);
     cgiMakeIntVarInRange(varName, cartHeight, "Height (in pixels) of track", 5, "4", "2500");
     puts("<BR>");
     }
 }
 
 static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			     char *name, boolean parentLevel)
 /* Show controls for haplotype-sorting display, which only makes sense to do when
  * the VCF file describes multiple genotypes. */
 {
 char *hapOrSample = vcfHaplotypeOrSample(cart);
 printf("<H3>%s sorting display</H3>\n", hapOrSample);
 vcfCfgHapClusterEnable(cart, tdb, name, parentLevel);
 vcfCfgHaplotypeMethod(cart, tdb, name, parentLevel, vcff);
 vcfCfgHapClusterTreeAngle(cart, tdb, name, parentLevel);
 vcfCfgHapClusterColor(cart, tdb, name, parentLevel);
 vcfCfgHapClusterHeight(cart, tdb, vcff, name, parentLevel);
 }
 
 static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			  char *name, boolean parentLevel)
 /* If checkbox is checked, apply minimum value filter to QUAL column. */
 {
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s." VCF_APPLY_MIN_QUAL_VAR, name);
 boolean applyFilter = cartOrTdbBoolean(cart, tdb, VCF_APPLY_MIN_QUAL_VAR,
 				       VCF_DEFAULT_APPLY_MIN_QUAL);
 cgiMakeCheckBox(cartVar, applyFilter);
 printf("<B>Exclude variants with Quality/confidence score (QUAL) score less than</B>\n");
 double minQual = cartOrTdbDouble(cart, tdb, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL);
 safef(cartVar, sizeof(cartVar), "%s." VCF_MIN_QUAL_VAR, name);
 cgiMakeDoubleVar(cartVar, minQual, 10);
 printf("<BR>\n");
 }
 
 static void vcfCfgFilterColumn(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			       char *name, boolean parentLevel)
 /* Show controls for filtering by value of VCF's FILTER column, which uses values defined
  * in the header. */
 {
 int filterCount = slCount(vcff->filterDefs);
 if (filterCount < 1)
     return;
 printf("<B>Exclude variants with these FILTER values:</B><BR>\n");
 char cartVar[1024];
 safef(cartVar, sizeof(cartVar), "%s."VCF_EXCLUDE_FILTER_VAR, name);
 if (slCount(vcff->filterDefs) > 1)
     {
     jsMakeCheckboxGroupSetClearButton(cartVar, TRUE);
     puts("&nbsp;");
     jsMakeCheckboxGroupSetClearButton(cartVar, FALSE);
     }
 char *values[filterCount];
 char *labels[filterCount];
 int i;
 struct vcfInfoDef *filt;
 for (i=0, filt=vcff->filterDefs;  filt != NULL;  i++, filt = filt->next)
     {
     values[i] = filt->key;
     struct dyString *dy = dyStringNew(0);
     dyStringAppend(dy, filt->key);
     if (isNotEmpty(filt->description))
 	dyStringPrintf(dy, " (%s)", filt->description);
     labels[i] = dyStringCannibalize(&dy);
     }
 struct slName *selectedValues = NULL;
 if (cartListVarExistsAnyLevel(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR))
     selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR);
 cgiMakeCheckboxGroupWithVals(cartVar, labels, values, filterCount, selectedValues, 1);
 }
 
 static void vcfCfgMinAlleleFreq(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 				char *name, boolean parentLevel)
 /* Show input for minimum allele frequency, if we can extract it from the VCF INFO column. */
 {
 printf("<B>Minimum minor allele frequency (if INFO column includes AF or AC+AN):</B>\n");
 double cartMinFreq = cartOrTdbDouble(cart, tdb, VCF_MIN_ALLELE_FREQ_VAR,
 				     VCF_DEFAULT_MIN_ALLELE_FREQ);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_MIN_ALLELE_FREQ_VAR, name);
 cgiMakeDoubleVarInRange(varName, cartMinFreq, "minor allele frequency between 0.0 and 0.5", 5,
 			"0.0", "0.5");
 puts("<BR>");
 }
 
+static struct slPair *vcfPhasedGetSamplesFromTdb(struct trackDb *tdb, boolean hideOtherSamples)
+/* Get the different VCF Phased Trio setings out of trackDb onto a list */
+{
+// cloneString here because we will be munging the result if there are alternate labels
+char *childSampleMaybeAlias = cloneString(trackDbLocalSetting(tdb, VCF_PHASED_CHILD_SAMPLE_SETTING));
+char *parentSamplesMaybeAlias = cloneString(trackDbLocalSetting(tdb, VCF_PHASED_PARENTS_SAMPLE_SETTING));
+char *samples[VCF_PHASED_MAX_OTHER_SAMPLES+1]; // for now only allow at most two parents
+int numOthers = 0;
+if (parentSamplesMaybeAlias && !hideOtherSamples)
+    {
+    numOthers = chopCommas(cloneString(parentSamplesMaybeAlias), samples);
+    if (numOthers > VCF_PHASED_MAX_OTHER_SAMPLES)
+        {
+        warn("More than %d other samples specified for phased trio", VCF_PHASED_MAX_OTHER_SAMPLES);
+        numOthers = VCF_PHASED_MAX_OTHER_SAMPLES;
+        }
+    // shove child into middle of array, and if there are two parents, scoot the second one to the end
+    int lastParentIx = VCF_PHASED_MAX_OTHER_SAMPLES - 1;
+    if (samples[lastParentIx] != NULL)
+        samples[VCF_PHASED_MAX_OTHER_SAMPLES] = cloneString(samples[lastParentIx]);
+    samples[lastParentIx] = cloneString(childSampleMaybeAlias);
+    }
+else
+    samples[0] = cloneString(childSampleMaybeAlias);
+
+boolean gotAlias = strchr(samples[0], '|') != NULL; // default to whatever is first
+struct slPair *ret = NULL;
+int i;
+for (i = 0; i < numOthers+1; i++)
+    {
+    char *val = strchr(samples[i], '|');
+    boolean foundAlias = val != NULL;
+    if (val != NULL)
+        {
+        if (foundAlias != gotAlias)
+            errAbort("Either all samples have aliases or none.");
+        else
+            *val++ = 0;
+        }
+    char *name = samples[i];
+    struct slPair *temp = slPairNew(cloneString(name), cloneString(val));
+    slAddHead(&ret, temp);
+    }
+slReverse(&ret);
+return ret;
+}
+
+struct slPair *vcfPhasedGetSampleOrder(struct cart *cart, struct trackDb *tdb)
+/* Parse out a trio sample order from either trackDb or the cart */
+{
+char sampleOrderVar[1028],hideParentsVar[1028];
+safef(sampleOrderVar, sizeof(sampleOrderVar), "%s.%s", tdb->track, VCF_PHASED_SAMPLE_ORDER_VAR);
+safef(hideParentsVar, sizeof(hideParentsVar), "%s.%s", tdb->track, VCF_PHASED_HIDE_OTHER_VAR);
+boolean hideOtherSamples = cartUsualBoolean(cart, hideParentsVar, FALSE);
+char *cartOrder = cartOptionalString(cart, sampleOrderVar);
+struct slPair *tdbOrder = vcfPhasedGetSamplesFromTdb(tdb,hideOtherSamples);
+if (cartOrder != NULL && !hideOtherSamples)
+    {
+    struct slName *name;
+    struct slName *fromCart = slNameListFromComma(cartOrder);
+    struct slPair *ret = NULL;
+    for (name = fromCart; name != NULL; name = name->next)
+        {
+        struct slPair *temp = slPairFind(tdbOrder, name->name);
+        slAddHead(&ret, temp);
+        }
+    slReverse(ret);
+    return ret;
+    }
+else
+    return tdbOrder;
+}
+
+static boolean hasSampleAliases(struct trackDb *tdb)
+/* Check whether trackDb has aliases for the sample names  */
+{
+struct slPair *nameVals = vcfPhasedGetSamplesFromTdb(tdb,FALSE);
+return nameVals->val != NULL;
+}
+
+static void vcfCfgPhasedTrioUi(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff, char *name)
+/* Put up the phased trio specific config settings */
+{
+if (hasSampleAliases(tdb))
+    {
+    printf("<b>Label samples by:</b>");
+    char defaultLabel[1024], aliasLabel[1024];
+    safef(defaultLabel, sizeof(defaultLabel), "%s.%s", tdb->track, VCF_PHASED_DEFAULT_LABEL_VAR);
+    safef(aliasLabel, sizeof(aliasLabel), "%s.%s", tdb->track, VCF_PHASED_ALIAS_LABEL_VAR);
+    boolean isDefaultChecked = cartUsualBoolean(cart, defaultLabel, TRUE);
+    boolean isAliasChecked = cartUsualBoolean(cart, aliasLabel, FALSE);
+    cgiMakeCheckBox(defaultLabel, isDefaultChecked);
+    printf("VCF file sample names &nbsp;");
+    cgiMakeCheckBox(aliasLabel, isAliasChecked);
+    printf("aliases");
+    printf("<br>");
+    }
+if (trackDbSetting(tdb,VCF_PHASED_PARENTS_SAMPLE_SETTING))
+    {
+    printf("<b>Hide parent/other sample(s)");
+    char hideVarName[1024];
+    safef(hideVarName, sizeof(hideVarName), "%s.%s", tdb->track, VCF_PHASED_HIDE_OTHER_VAR);
+    boolean hidingOtherSamples = cartUsualBoolean(cart, hideVarName, FALSE);
+    cgiMakeCheckBox(hideVarName, hidingOtherSamples);
+    }
+}
+
 void vcfCfgUi(struct cart *cart, struct trackDb *tdb, char *name, char *title, boolean boxed)
 /* VCF: Variant Call Format.  redmine #3710 */
 {
 boxed = cfgBeginBoxAndTitle(tdb, boxed, title);
 printf("<TABLE%s><TR><TD>", boxed ? " width='100%'" : "");
 struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb);
 if (vcff != NULL)
     {
     boolean parentLevel = isNameAtParentLevel(tdb, name);
-    if (vcff->genotypeCount > 1)
+    if (vcff->genotypeCount > 1 && !sameString(tdb->type, "vcfPhasedTrio"))
 	{
 	vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel);
 	}
+    if (sameString(tdb->type, "vcfPhasedTrio"))
+        {
+        vcfCfgPhasedTrioUi(cart, tdb, vcff, name);
+        }
     if (differentString(tdb->track,"evsEsp6500"))
         {
         puts("<H3>Filters</H3>");
         vcfCfgMinQual(cart, tdb, vcff, name, parentLevel);
         vcfCfgFilterColumn(cart, tdb, vcff, name, parentLevel);
         }
     vcfCfgMinAlleleFreq(cart, tdb, vcff, name, parentLevel);
     }
 else
     {
     printf("Sorry, couldn't access VCF file.<BR>\n");
     }
 
 puts("</TD>");
 if (boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
     printf("<TD style='text-align:right'><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" "
            "TARGET=_BLANK>VCF configuration help</A></TD>");
 
 printf("</TR></TABLE>");
 
 if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp")))
     printf("<P><A HREF=\"../goldenPath/help/hgVcfTrackHelp.html\" TARGET=_BLANK>VCF "
 	   "configuration help</A></P>");
 cfgEndBox(boxed);
 }