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
@@ -1,95 +1,96 @@
 // alleles - common Gene haplotype alleles. */
 
 #include "common.h"
 #include "web.h"
 #include "genePredReader.h"
 #include "vcf.h"
 #include "haplotypes.h"
 #include "hgGene.h"
 
 static boolean allelesExists(struct section *section,
         struct sqlConnection *conn, char *geneId)
 // Return TRUE if common haplotype alleles exist.
 {
 // If there was a reset then clear out settings
 if (cartUsualBoolean(cart, HAPLO_RESET_ALL, FALSE))
     cartRemovePrefix(cart,HAPLO_TABLE "_" );
 
 // 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);
 
 // All or Limit to the 99%
 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 );
     }
 
 // Need to generate haplotypes
 section->items = geneHapSetForOneModel(he,vcff,gp,TRUE);
 
 return TRUE;// (section->items != NULL);
 }
 
 static void allelesPrint(struct section *section,
 	struct sqlConnection *conn, char *geneId)
 // Print out common gene haplotype alleles.
 {
 struct haploExtras *he = section->extras;
 struct haplotypeSet *hapSet = section->items;
 geneAllelesTableAndControls(cart, geneId, he, hapSet);
 
 haplotypeExtrasFree(&he);
 }
 
 struct section *allelesSection(struct sqlConnection *conn, struct hash *sectionRa)
 // Create UCSC KG Method section.
 {
 struct section *section = sectionNew(sectionRa, HGG_GENE_ALLELES);
 if (section != NULL)
     {
     section->exists = allelesExists;
     section->print = allelesPrint;
     }
 return section;
 }