c9d17a52b6b5663c7175b01f801d23198b675f7e
max
  Fri Sep 25 12:03:55 2026 -0700
Revert all bigBed-filters for VCF changes, as Chris did that earlier already.

This reverts commit 2521d696f5073ce8cee3f59f423f161fdb77d550.

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index cc773906eb1..7ba16bd1580 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -2,31 +2,30 @@
  * between more than one CGI. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ 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"
-#include "asParse.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. */
 {
@@ -184,31 +183,31 @@
               "if (this.value == '"VCF_HAP_METHOD_CENTER_WEIGHTED"') {"
               "  $('#leafShapeContainer').show();"
               "  $('#sampleColorContainer').hide();"
               "} else if (this.value == '"VCF_HAP_METHOD_TREE_FILE"') {"
               "  $('#sampleColorContainer').show();"
               "  $('#leafShapeContainer').hide();"
               "} else {"
               "  $('#sampleColorContainer').hide();"
               "  $('#leafShapeContainer').hide();"
               "}});\n",
               varName);
     }
 }
 
 //TODO: share this code w/hgTracks, hgc in hg/lib/vcfFile.c
-static struct vcfFile *vcfHopefullyOpenHeaderUncached(struct cart *cart, struct trackDb *tdb)
+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);
@@ -234,93 +233,30 @@
     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 struct vcfFile *vcfHopefullyOpenHeader(struct cart *cart, struct trackDb *tdb)
-/* Return the vcfFile object with header data, or NULL, opening the file only once per track
- * in this CGI run: the config UI and the generic trackDb filter code both need the header. */
-{
-static struct hash *vcffCache = NULL;
-if (vcffCache == NULL)
-    vcffCache = hashNew(0);
-struct hashEl *hel = hashLookup(vcffCache, tdb->track);
-if (hel != NULL)
-    return hel->val;
-struct vcfFile *vcff = vcfHopefullyOpenHeaderUncached(cart, tdb);
-hashAdd(vcffCache, tdb->track, vcff);
-return vcff;
-}
-
-static struct asColumn *vcfFilterAsColumn(char *name, char *comment, char *asType)
-/* Make one pseudo-autoSql column for vcfInfoAsObj. */
-{
-struct asColumn *col;
-AllocVar(col);
-col->name = cloneString(name);
-col->comment = cloneString(isNotEmpty(comment) ? comment : name);
-col->lowType = asTypeFindLow(asType);
-return col;
-}
-
-struct asObject *vcfInfoAsObj(struct cart *cart, struct trackDb *tdb)
-/* Return a pseudo-autoSql object that describes the fields of a VCF track that can be used by the
- * generic trackDb filters (filter.*, filterText.*, filterValues.* etc): one column per INFO
- * definition in the VCF header, named by the INFO key, with the header's Description as comment,
- * followed by the fixed columns ID and QUAL.  Returns NULL if the file cannot be opened. */
-{
-struct vcfFile *vcff = vcfHopefullyOpenHeader(cart, tdb);
-if (vcff == NULL)
-    return NULL;
-struct asObject *asObj;
-AllocVar(asObj);
-asObj->name = cloneString("vcfInfo");
-asObj->comment = cloneString("VCF INFO fields");
-struct hash *seen = hashNew(0);
-struct vcfInfoDef *def;
-for (def = vcff->infoDefs;  def != NULL;  def = def->next)
-    {
-    char *asType = "string";
-    if (def->type == vcfInfoInteger || def->type == vcfInfoFlag)
-        asType = "int";
-    else if (def->type == vcfInfoFloat)
-        asType = "double";
-    else if (def->type == vcfInfoCharacter)
-        asType = "char";
-    slAddHead(&asObj->columnList, vcfFilterAsColumn(def->key, def->description, asType));
-    hashStore(seen, def->key);
-    }
-// If an INFO key has the same name as a fixed column, the INFO field wins, also in hgTracks
-if (!hashLookup(seen, "ID"))
-    slAddHead(&asObj->columnList, vcfFilterAsColumn("ID", "Variant ID", "string"));
-if (!hashLookup(seen, "QUAL"))
-    slAddHead(&asObj->columnList, vcfFilterAsColumn("QUAL", "Quality score (QUAL)", "double"));
-slReverse(&asObj->columnList);
-hashFree(&seen);
-return asObj;
-}
-
 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. */
 {
@@ -787,32 +723,30 @@
         {
         vcfCfgPhasedTrioUi(cart, tdb, vcff, name, parentLevel);
         }
     if (differentString(tdb->track,"evsEsp6500") && (doVcfFilterUi || doVcfQualUi))
         {
         puts("<H3>Filters</H3>");
         if (doVcfQualUi)
             vcfCfgMinQual(cart, tdb, vcff, name, parentLevel);
         if (doVcfFilterUi)
             vcfCfgFilterColumn(cart, tdb, vcff, name, parentLevel);
         }
     if (doVcfMafUi)
         vcfCfgMinAlleleFreq(cart, tdb, vcff, name, parentLevel);
     if (doVcfMinAcUi)
         vcfCfgMinAc(cart, tdb, vcff, name, parentLevel);
-    // The generic trackDb filters (filter.<INFO key>, filterValues.<INFO key>, ...), same UI as bigBed
-    trackDbFiltersCfgUi(cartString(cart, "db"), cart, tdb, name, FALSE);
     }
 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>");
 wigOption(cart, name, title, tdb);
 
 if (!boxed && fileExists(hHelpFile("hgVcfTrackHelp")))