e62655df7abb8c2ab44f5b11798f6f6c731afded
angie
  Wed Oct 5 15:42:05 2011 -0700
Feature #3710 (vcfTabix UI options): added optional filter on min QUAL score.
diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index fb16ef3..171e5ae 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -148,33 +148,33 @@
     {
     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 compositeLevel)
 /* Let the user enable/disable haplotype sorting display. */
 {
 printf("<B>Enable Haplotype sorting display: </B>");
 boolean hapClustEnabled = cartUsualBooleanClosestToHome(cart, tdb, compositeLevel,
 							VCF_HAP_ENABLED_VAR, TRUE);
-char varName[1024];
-safef(varName, sizeof(varName), "%s." VCF_HAP_ENABLED_VAR, name);
-cgiMakeCheckBox(varName, hapClustEnabled);
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s." VCF_HAP_ENABLED_VAR, name);
+cgiMakeCheckBox(cartVar, hapClustEnabled);
 printf("<BR>\n");
 }
 
 static void vcfCfgHapClusterColor(struct cart *cart, struct trackDb *tdb, char *name,
 				   boolean compositeLevel)
 /* Let the user choose how to color the sorted haplotypes. */
 {
 printf("<B>Color sorted haplotypes by:</B>\n");
 char *colorBy = cartUsualStringClosestToHome(cart, tdb, compositeLevel,
 					     VCF_HAP_COLORBY_VAR, VCF_HAP_COLORBY_REFALT);
 boolean colorByRefAlt = sameString(colorBy, VCF_HAP_COLORBY_REFALT);
 char varName[1024];
 safef(varName, sizeof(varName), "%s." VCF_HAP_COLORBY_VAR, name);
 cgiMakeRadioButton(varName, VCF_HAP_COLORBY_REFALT, colorByRefAlt);
 printf("reference/alternate alleles (reference = blue, alternate = red)\n");
@@ -198,41 +198,58 @@
 }
 
 static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
 			     char *name, boolean compositeLevel)
 /* Show controls for haplotype-sorting display, which only makes sense to do when
  * the VCF file describes multiple genotypes. */
 {
 vcfCfgHapClusterEnable(cart, tdb, name, compositeLevel);
 vcfCfgHaplotypeCenter(cart, tdb, vcff, NULL, NULL, 0, "mainForm");
 vcfCfgHapClusterColor(cart, tdb, name, compositeLevel);
 vcfCfgHapClusterHeight(cart, tdb, vcff, name, compositeLevel);
 //      thicken lines?
 //      outline center variant?
 }
 
+static void vcfCfgMinQual(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
+			  char *name, boolean compositeLevel)
+/* 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, compositeLevel,
+					VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL);
+cgiMakeCheckBox(cartVar, applyFilter);
+printf("<B>Exclude items with QUAL score less than &nbsp;</B>\n");
+double minQual = cartUsualDoubleClosestToHome(cart, tdb, compositeLevel, 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 compositeLevel)
 /* 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 items with these FILTER settings:</B><BR>\n");
-char cartVar[512];
-safef(cartVar, sizeof(cartVar), "%s.exclude_filterColumn", name);
+printf("<B>Exclude items with these FILTER values:</B><BR>\n");
+char cartVar[1024];
+safef(cartVar, sizeof(cartVar), "%s."VCF_EXCLUDE_FILTER_VAR, name);
 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);
@@ -242,30 +259,31 @@
     selectedValues = cartOptionalSlNameList(cart, cartVar);
 cgiMakeCheckboxGroupWithVals(cartVar, labels, values, filterCount, selectedValues, 1);
 }
 
 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 compositeLevel = isNameAtCompositeLevel(tdb, name);
     if (vcff->genotypeCount > 1)
 	vcfCfgHapCluster(cart, tdb, vcff, name, compositeLevel);
+    vcfCfgMinQual(cart, tdb, vcff, name, compositeLevel);
     vcfCfgFilterColumn(cart, tdb, vcff, name, compositeLevel);
     }
 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")))