static boolean getMinQual(struct trackDb *tdb, double *retMinQual) /* Return TRUE and set retMinQual if cart contains minimum QUAL filter */ { if (cartOrTdbBoolean(cart, tdb, VCF_APPLY_MIN_QUAL_VAR, VCF_DEFAULT_APPLY_MIN_QUAL)) { if (retMinQual != NULL) *retMinQual = cartOrTdbDouble(cart, tdb, VCF_MIN_QUAL_VAR, VCF_DEFAULT_MIN_QUAL); return TRUE; } return FALSE; }
static void vcfTabixLoadItems(struct track *tg) /* Load items in window from VCF file using its tabix index file. */ { char *fileOrUrl = NULL; /* Figure out url or file name. */ if (tg->parallelLoading) { /* do not use mysql during parallel-fetch load */ fileOrUrl = trackDbSetting(tg->tdb, "bigDataUrl"); } else { struct sqlConnection *conn = hAllocConnTrack(database, tg->tdb); fileOrUrl = bbiNameFromSettingOrTableChrom(tg->tdb, conn, tg->table, chromName); hFreeConn(&conn); } if (isEmpty(fileOrUrl)) return; int vcfMaxErr = -1; struct vcfFile *vcff = NULL; boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE); /* protect against temporary network error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { vcff = vcfTabixFileMayOpen(fileOrUrl, chromName, winStart, winEnd, vcfMaxErr, -1); if (vcff != NULL) { filterRecords(vcff, tg->tdb); if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 && (tg->visibility == tvPack || tg->visibility == tvSquish)) vcfHapClusterOverloadMethods(tg, vcff); else { tg->items = vcfFileToPgSnp(vcff, tg->tdb); // pgSnp bases coloring/display decision on count of items: tg->customInt = slCount(tg->items); } // Don't vcfFileFree here -- we are using its string pointers! } } errCatchEnd(errCatch); if (errCatch->gotError || vcff == NULL) { if (isNotEmpty(errCatch->message->string)) tg->networkErrMsg = cloneString(errCatch->message->string); tg->drawItems = bigDrawWarning; tg->totalHeight = bigWarnTotalHeight; } errCatchFree(&errCatch); }
static void vcfLoadItems(struct track *tg) /* Load items in window from VCF file. */ { int vcfMaxErr = -1; struct vcfFile *vcff = NULL; boolean hapClustEnabled = cartOrTdbBoolean(cart, tg->tdb, VCF_HAP_ENABLED_VAR, TRUE); char *table = tg->table; struct customTrack *ct = tg->customPt; struct sqlConnection *conn; if (ct == NULL) conn = hAllocConnTrack(database, tg->tdb); else { conn = hAllocConn(CUSTOM_TRASH); table = ct->dbTableName; } char *vcfFile = bbiNameFromSettingOrTable(tg->tdb, conn, table); hFreeConn(&conn); /* protect against parse error */ struct errCatch *errCatch = errCatchNew(); if (errCatchStart(errCatch)) { vcff = vcfFileMayOpen(vcfFile, chromName, winStart, winEnd, vcfMaxErr, -1, TRUE); if (vcff != NULL) { filterRecords(vcff, tg->tdb); if (hapClustEnabled && vcff->genotypeCount > 1 && vcff->genotypeCount < 3000 && (tg->visibility == tvPack || tg->visibility == tvSquish)) vcfHapClusterOverloadMethods(tg, vcff); else { tg->items = vcfFileToPgSnp(vcff, tg->tdb); // pgSnp bases coloring/display decision on count of items: tg->customInt = slCount(tg->items); } // Don't vcfFileFree here -- we are using its string pointers! } } errCatchEnd(errCatch); if (errCatch->gotError || vcff == NULL) { if (isNotEmpty(errCatch->message->string)) tg->networkErrMsg = cloneString(errCatch->message->string); tg->drawItems = bigDrawWarning; tg->totalHeight = bigWarnTotalHeight; } errCatchFree(&errCatch); }
static void vcfRecordDetails(struct trackDb *tdb, struct vcfRecord *rec) /* Display the contents of a single line of VCF, assumed to be from seqName * (using seqName instead of rec->chrom because rec->chrom might lack "chr"). */ { printf("<B>Name:</B> %s<BR>\n", rec->name); // Since these are variants, if it looks like a dbSNP or dbVar ID, provide a link: if (regexMatch(rec->name, "^rs[0-9]+$")) { printf("<B>dbSNP:</B> "); printDbSnpRsUrl(rec->name, "%s", rec->name); puts("<BR>"); } else if (regexMatch(rec->name, "^[en]ss?v[0-9]+$")) { printf("<B>dbVar:</B> "); printf("<A HREF=\"http://www.ncbi.nlm.nih.gov/dbvar/variants/%s/\" " "TARGET=_BLANK>%s</A><BR>\n", rec->name, rec->name); } printCustomUrl(tdb, rec->name, TRUE); boolean hapClustEnabled = cartOrTdbBoolean(cart, tdb, VCF_HAP_ENABLED_VAR, TRUE); if (hapClustEnabled) { static char *formName = "vcfCfgHapCenter"; printf("<FORM NAME=\"%s\" ACTION=\"%s\">\n", formName, hgTracksName()); cartSaveSession(cart); vcfCfgHaplotypeCenter(cart, tdb, tdb->track, FALSE, rec->file, rec->name, seqName, rec->chromStart, formName); printf("</FORM>\n"); } char leftBase = rec->alleles[0][0]; unsigned int vcfStart = vcfRecordTrimIndelLeftBase(rec); boolean showLeftBase = (rec->chromStart == vcfStart+1); (void)vcfRecordTrimAllelesRight(rec); char *displayAls[rec->alleleCount]; makeDisplayAlleles(rec, showLeftBase, leftBase, 20, TRUE, FALSE, displayAls); printPosOnChrom(seqName, rec->chromStart, rec->chromEnd, NULL, FALSE, rec->name); printf("<B>Reference allele:</B> %s<BR>\n", displayAls[0]); vcfAltAlleleDetails(rec, displayAls); vcfQualDetails(rec); vcfFilterDetails(rec); vcfInfoDetails(rec); pgSnpCodingDetail(rec); makeDisplayAlleles(rec, showLeftBase, leftBase, 5, FALSE, TRUE, displayAls); vcfGenotypesDetails(rec, tdb, displayAls); }
static void vcfGenotypesDetails(struct vcfRecord *rec, struct trackDb *tdb, char **displayAls) /* Print summary of allele and genotype frequency, plus collapsible section * with table of genotype details. */ { struct vcfFile *vcff = rec->file; if (vcff->genotypeCount == 0) return; // Wrapper table for collapsible section: puts("<TABLE>"); pushWarnHandler(ignoreEm); vcfParseGenotypes(rec); popWarnHandler(); // Tally genotypes and alleles for summary: int refs = 0, alts = 0, unks = 0; int refRefs = 0, refAlts = 0, altAlts = 0, gtUnk = 0, gtOther = 0, phasedGts = 0; int i; for (i = 0; i < vcff->genotypeCount; i++) { struct vcfGenotype *gt = &(rec->genotypes[i]); if (gt->isPhased) phasedGts++; if (gt->hapIxA == 0) refs++; else if (gt->hapIxA > 0) alts++; else unks++; if (!gt->isHaploid) { if (gt->hapIxB == 0) refs++; else if (gt->hapIxB > 0) alts++; else unks++; if (gt->hapIxA == 0 && gt->hapIxB == 0) refRefs++; else if (gt->hapIxA == 1 && gt->hapIxB == 1) altAlts++; else if ((gt->hapIxA == 1 && gt->hapIxB == 0) || (gt->hapIxA == 0 && gt->hapIxB == 1)) refAlts++; else if (gt->hapIxA < 0 || gt->hapIxB < 0) gtUnk++; else gtOther++; } } printf("<B>Genotype count:</B> %d", vcff->genotypeCount); if (differentString(seqName, "chrY")) printf(" (%d phased)", phasedGts); else printf(" (haploid)"); puts("<BR>"); int totalAlleles = refs + alts + unks; double refAf = (double)refs/totalAlleles; double altAf = (double)alts/totalAlleles; printf("<B>Alleles:</B> %s: %d (%.3f%%); %s: %d (%.3f%%)", displayAls[0], refs, 100*refAf, displayAls[1], alts, 100*altAf); if (unks > 0) printf("; unknown: %d (%.3f%%)", unks, 100 * (double)unks/totalAlleles); puts("<BR>"); // Should be a better way to detect haploid chromosomes than comparison with "chrY": if (vcff->genotypeCount > 1 && differentString(seqName, "chrY")) { printf("<B>Genotypes:</B> %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%); %s/%s: %d (%.3f%%)", displayAls[0], displayAls[0], refRefs, 100*(double)refRefs/vcff->genotypeCount, displayAls[0], displayAls[1], refAlts, 100*(double)refAlts/vcff->genotypeCount, displayAls[1], displayAls[1], altAlts, 100*(double)altAlts/vcff->genotypeCount); if (gtUnk > 0) printf("; unknown: %d (%.3f%%)", gtUnk, 100*(double)gtUnk/vcff->genotypeCount); if (gtOther > 0) printf("; other: %d (%.3f%%)", gtOther, 100*(double)gtOther/vcff->genotypeCount); printf("<BR>\n"); if (rec->alleleCount == 2) { boolean showHW = cartOrTdbBoolean(cart, tdb, VCF_SHOW_HW_VAR, FALSE); if (showHW) printf("<B><A HREF=\"http://en.wikipedia.org/wiki/Hardy%%E2%%80%%93Weinberg_principle\" " "TARGET=_BLANK>Hardy-Weinberg equilibrium</A>:</B> " "P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%; P(%s/%s) = %.3f%%<BR>", displayAls[0], displayAls[0], 100*refAf*refAf, displayAls[0], displayAls[1], 100*2*refAf*altAf, displayAls[1], displayAls[1], 100*altAf*altAf); } } puts("<BR>"); vcfGenotypeTable(rec, tdb->track, displayAls); puts("</TABLE>"); }