eb51fcb6dee7a48c1a98e7d12db7c4bd380bf54f
tdreszer
  Fri May 10 17:22:46 2013 -0700
Fixed 2 objscure bugs resulting from deletions overlapping each other.  Also did some name changing and comment clarification suggested by Angie.
diff --git src/hg/hgGene/alleles.c src/hg/hgGene/alleles.c
index 4ad5ecc..9e7925f 100644
--- src/hg/hgGene/alleles.c
+++ src/hg/hgGene/alleles.c
@@ -18,30 +18,31 @@
 // Start with the default variables for haplotype retrieval
 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
 
 // 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);