007cb48e6924935c046a7a0d0354eeac84e5f6cb
angie
  Wed Oct 5 11:30:12 2011 -0700
Feature #3710 (vcfTabix UI options): added filtering by value of FILTER column.
diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 2473e2a..fb16ef3 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -1,23 +1,24 @@
 /* vcfUi - Variant Call Format user interface controls that are shared
  * between more than one CGI. */
 
 #include "common.h"
 #include "cheapcgi.h"
 #include "errCatch.h"
 #include "hCommon.h"
 #include "hui.h"
+#include "jsHelper.h"
 #include "vcf.h"
 #include "vcfUi.h"
 #if (defined USE_TABIX && defined KNETFILE_HOOKS)
 #include "knetUdc.h"
 #include "udc.h"
 #endif//def USE_TABIX && KNETFILE_HOOKS
 
 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;
 }
 
@@ -185,63 +186,91 @@
 				   char *name, boolean compositeLevel)
 /* 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, compositeLevel,
 					       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, "10", "2500");
     }
 }
 
 static void vcfCfgHapCluster(struct cart *cart, struct trackDb *tdb, struct vcfFile *vcff,
-			     char *name)
+			     char *name, boolean compositeLevel)
 /* Show controls for haplotype-sorting display, which only makes sense to do when
  * the VCF file describes multiple genotypes. */
 {
-boolean compositeLevel = isNameAtCompositeLevel(tdb, name);
 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?
-//      color haplotypes by red/blue or allele bases?
+}
+
+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);
+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 (cartListVarExists(cart, cartVar))
+    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);
+	vcfCfgHapCluster(cart, tdb, vcff, name, compositeLevel);
+    vcfCfgFilterColumn(cart, tdb, vcff, name, compositeLevel);
     }
 else
     {
     printf("Sorry, couldn't access VCF file.<BR>\n");
     }
 
-// filter:
-//   by qual column
-//   by filter column
-// color bases like pgSnp or some better palette?
-
 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);
 }