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; }