da43847aab52991e91bfec700b16038710710038
max
  Sat Sep 26 21:56:05 2026 -0700
VCF tracks: new trackDb setting excludeFilterValues, a comma-separated list of FILTER values that are hidden by default; they show up pre-checked in the existing Exclude variants with these FILTER values list, refs #38424

diff --git src/hg/lib/vcfUi.c src/hg/lib/vcfUi.c
index 21f29b1995c..a6d4968cf3d 100644
--- src/hg/lib/vcfUi.c
+++ src/hg/lib/vcfUi.c
@@ -985,30 +985,37 @@
 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 (cartListVarExistsAnyLevel(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR))
     selectedValues = cartOptionalSlNameListClosestToHome(cart, tdb, FALSE, VCF_EXCLUDE_FILTER_VAR);
+else
+    {
+    // trackDb can set the default, e.g. to hide artifact-flagged records
+    char *tdbDefault = trackDbSettingClosestToHome(tdb, VCF_EXCLUDE_FILTER_VAR);
+    if (isNotEmpty(tdbDefault))
+        selectedValues = slNameListFromComma(tdbDefault);
+    }
 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 = 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>");