5e1673a9fadc12f17211b01376f538598f6bb525
chmalee
  Wed Jul 15 11:43:26 2020 -0700
Adding some trackDb options to hide some VCF config options that are useless for 1000 genomes and sars-cov-2 vcfs, refs #24317

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 52a7e2f..7073178 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -618,44 +618,50 @@
 char *infoText = "Check this box to color child variants red if they do not agree with the implied "
     "parental transmitted allele at this location. This configuration is only available when parent "
     "haplotypes are displayed.";
 printInfoIcon(infoText);
 }
 
 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);
+    boolean doVcfFilterUi = cartOrTdbBoolean(cart, tdb, VCF_DO_FILTER_UI, TRUE);
+    boolean doVcfQualUi = cartOrTdbBoolean(cart, tdb, VCF_DO_QUAL_UI, TRUE);
+    boolean doVcfMafUi = cartOrTdbBoolean(cart, tdb, VCF_DO_MAF_UI, TRUE);
     if (vcff->genotypeCount > 1 && !sameString(tdb->type, "vcfPhasedTrio"))
         {
         vcfCfgHapCluster(cart, tdb, vcff, name, parentLevel);
         }
     if (sameString(tdb->type, "vcfPhasedTrio"))
         {
         vcfCfgPhasedTrioUi(cart, tdb, vcff, name, parentLevel);
         }
-    if (differentString(tdb->track,"evsEsp6500"))
+    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);
     }
 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")))