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);