2f18fa9e25b5791684083c159a155694f105288a
tdreszer
  Mon May 13 14:26:51 2013 -0700
Fixed Synonymous variant sorting, changed full sequence and all variant cart vars to global (instead of gene specific) and conditionally added the haplotype ID to a hover message at Kate's request.
diff --git src/hg/hgGene/alleles.c src/hg/hgGene/alleles.c
index 9e7925f..66b5a1e 100644
--- src/hg/hgGene/alleles.c
+++ src/hg/hgGene/alleles.c
@@ -19,48 +19,48 @@
 struct haploExtras *he = haplotypeExtrasDefault(database, 0);
 section->extras = he;
 
 // Need to get genePred struct from geneId
 char where[128];
 safef(where,sizeof(where),"name = '%s'",geneId);
 struct genePred *gp = genePredReaderLoadQuery(conn,he->geneTable, where);
 if (gp == NULL || gp->cdsStart == gp->cdsEnd)  // Ain't interested in non-protein coding genes
     {
     haplotypeExtrasFree(&he);
     return FALSE;
     }
 
 he->chrom = gp->chrom; // Probably not needed
 he->justModel = lmCloneString(he->lm,geneId);
-he->growTree = FALSE; // Tree growing not needed here
+//he->growTree = FALSE; // Tree growing not needed here
 
 // 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 =  sameOk(geneId,cartOptionalString(cart, HAPLO_RARE_VAR));
+boolean rareVars =  cartUsualBoolean(cart, HAPLO_RARE_VAR, FALSE);
 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 );
     }