0cbeed8fcb8eccd05e18cea41d4954f20d7698bd
angie
  Wed Jul 9 13:45:50 2014 -0700
Added trackDb settings for initializing VCF track controls.This will be useful for CTs/hub tracks to turn off haplotype clustering
or apply minimum QUAL score / minimum minor allele frequency filters.

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 16dabd7..0ef5dde 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -161,112 +161,107 @@
     }
 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 = cartUsualBooleanClosestToHome(cart, tdb, parentLevel,
-							VCF_HAP_ENABLED_VAR, TRUE);
+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");
 }
 
 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");
-char *colorBy = cartUsualStringClosestToHome(cart, tdb, parentLevel,
-					     VCF_HAP_COLORBY_VAR, VCF_DEFAULT_HAP_COLORBY);
+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");
-char *treeAngle = cartUsualStringClosestToHome(cart, tdb, parentLevel,
-					     VCF_HAP_TREEANGLE_VAR, VCF_DEFAULT_HAP_TREEANGLE);
+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");
 cgiMakeRadioButton(varName, VCF_HAP_TREEANGLE_RECTANGLE,
 		   sameString(treeAngle, VCF_HAP_TREEANGLE_RECTANGLE));
 printf("draw leaf clusters as [<BR>\n");
 }
 
 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");
-    int cartHeight = cartUsualIntClosestToHome(cart, tdb, parentLevel,
-					       VCF_HAP_HEIGHT_VAR, VCF_DEFAULT_HAP_HEIGHT);
+    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. */
 {
 vcfCfgHapClusterEnable(cart, tdb, name, parentLevel);
 vcfCfgHaplotypeCenter(cart, tdb, name, parentLevel, vcff, NULL, NULL, 0, "mainForm");
 vcfCfgHapClusterColor(cart, tdb, name, parentLevel);
 vcfCfgHapClusterTreeAngle(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 = cartUsualBooleanClosestToHome(cart, tdb, parentLevel,
-					VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL);
+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 = cartUsualDoubleClosestToHome(cart, tdb, parentLevel, VCF_MIN_QUAL_VAR,
-					      VCF_DEFAULT_MIN_QUAL);
+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];
@@ -286,32 +281,32 @@
     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 = cartUsualDoubleClosestToHome(cart, tdb, parentLevel,
-					   VCF_MIN_ALLELE_FREQ_VAR, VCF_DEFAULT_MIN_ALLELE_FREQ);
+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)
     {