71d39e8c3adf5f08cfc12d64d72c53919a701f5f
tdreszer
  Fri May 10 09:38:00 2013 -0700
A couple of cart vars got screwed up in the last change to no longer support timeout vars.
diff --git src/hg/hgGene/alleles.c src/hg/hgGene/alleles.c
index b311166..4ad5ecc 100644
--- src/hg/hgGene/alleles.c
+++ src/hg/hgGene/alleles.c
@@ -35,31 +35,31 @@
 // Need to determine the correct vcf file and open it
 if (haplotypesDiscoverVcfFile(he, gp->chrom) == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 struct vcfFile *vcff = vcfTabixFileMayOpen(he->inFile, NULL, 0, 0,VCF_IGNORE_ERRS, 0);
 if (vcff == NULL)
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 vcfFileMakeReusePool(vcff,1024 * 1024);
 
 // All or Limit to the 99%
-boolean rareVars = cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
+boolean rareVars =  sameOk(geneId,cartOptionalString(cart, HAPLO_RARE_VAR));
 if (rareVars)
     he->synonymous = TRUE;
 else
     he->variantMinPct = HAPLO_COMMON_VARIANT_MIN_PCT;
 
 // Lets show the population distribution
 he->populationsToo   = cartUsualBoolean(cart, HAPLO_MAJOR_DIST, FALSE);
 he->populationsMinor = cartUsualBoolean(cart, HAPLO_MINOR_DIST, FALSE);
 if (he->populationsToo)
     he->populationMinPct = 5;
 else if (he->populationsMinor)
     {
     he->populationsMinor = FALSE;
     cartRemove(cart, HAPLO_MINOR_DIST );
     }