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/lib/vcfUi.c src/hg/lib/vcfUi.c
index 7cfd5e8..045f92c 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -1,388 +1,425 @@
 /* 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>To anchor the sorting to a particular variant, "
+            {
+	    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>Haplotype sorting order:</B></TD></TR><TR><TD>\n");
+	   "<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");
-    // If trackDb specifies a treeFile, offer that as an option
-    char *hapMethodTdb = trackDbSetting(tdb, VCF_HAP_METHOD_VAR);
-    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");
-        }
-    puts("</TD></TR></TABLE>");
+    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 Haplotype sorting display</B><BR>\n");
+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>Haplotype coloring scheme:</B><BR>\n");
+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. */
 {
-printf("<B>Haplotype clustering tree leaf shape:</B><BR>\n");
+// 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 leaf clusters as &lt;<BR>\n");
+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 leaf clusters as [<BR>\n");
+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>Haplotype sorting display height:</B> \n");
+    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);
-vcfCfgHapClusterColor(cart, tdb, name, parentLevel);
 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>");
 }
 
 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)
 	{
-	puts("<H3>Haplotype sorting display</H3>");
-	puts("<P>When this display mode is enabled and genotypes are phased or homozygous, "
-	     "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.</P>");
 	vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel);
 	}
     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);
 }