04a89671eb368a9fac4b5b1999ff4b55b13337a8 angie Tue Sep 17 07:17:49 2013 -0700 Yikes, when querying at the cart position instead of the whole genome,annoStreamVcf was skipping rows that it shouldn't have! diff --git src/lib/annoStreamVcf.c src/lib/annoStreamVcf.c index 2ed7b19..6626be4 100644 --- src/lib/annoStreamVcf.c +++ src/lib/annoStreamVcf.c @@ -1,211 +1,211 @@ /* annoStreamVcf -- subclass of annoStreamer for VCF files */ #include "annoStreamVcf.h" #include "twoBit.h" #include "vcf.h" struct annoStreamVcf { struct annoStreamer streamer; // Parent class members & methods // Private members struct vcfFile *vcff; // VCF parsed header and file object struct vcfRecord *record; // Current parsed row of VCF (need this for chromEnd) char *asWords[VCF_NUM_COLS]; // Current row of VCF with genotypes squashed for autoSql struct dyString *dyGt; // Scratch space for squashing genotype columns struct hash *chromNameHash; // Translate "chr"-less seq names if necessary. int numCols; // Number of columns in autoSql def of VCF. int numFileCols; // Number of columns in VCF file. boolean isTabix; // True if we are accessing compressed VCF via tabix index int maxRecords; // Maximum number of annoRows to return. int recordCount; // Number of annoRows we have returned so far. }; static void asvSetRegion(struct annoStreamer *vSelf, char *chrom, uint regionStart, uint regionEnd) /* Set region -- and free current sqlResult if there is one. */ { annoStreamerSetRegion(vSelf, chrom, regionStart, regionEnd); struct annoStreamVcf *self = (struct annoStreamVcf *)vSelf; if (self->isTabix) lineFileSetTabixRegion(self->vcff->lf, chrom, regionStart, regionEnd); } static char *asvGetHeader(struct annoStreamer *vSelf) /* Return VCF header (e.g. for use by formatter) */ { struct annoStreamVcf *self = (struct annoStreamVcf *)vSelf; return cloneString(self->vcff->headerString); } static char **nextRowRaw(struct annoStreamVcf *self) /* Get the next VCF record and put the row text into autoSql words. * Return pointer to self->asWords if we get a row, otherwise NULL. */ { char *words[self->numFileCols]; int wordCount; if ((wordCount = lineFileChop(self->vcff->lf, words)) <= 0) return NULL; lineFileExpectWords(self->vcff->lf, self->numFileCols, wordCount); int i; // First 8 columns are always in the VCF file: for (i = 0; i < 8; i++) { freeMem(self->asWords[i]); self->asWords[i] = cloneString(words[i]); } // Depending on whether VCF contains genotypes, number of file columns may be // smaller or larger than number of autoSql columns: if (self->vcff->genotypeCount > 0) { self->asWords[8] = words[8]; dyStringClear(self->dyGt); for (i = 0; i < self->vcff->genotypeCount; i++) { if (i > 0) dyStringAppendC(self->dyGt, '\t'); dyStringAppend(self->dyGt, words[9+i]); } self->asWords[9] = self->dyGt->string; } else { self->asWords[8] = ""; self->asWords[9] = ""; } self->record = vcfRecordFromRow(self->vcff, words); return self->asWords; } static char *getProperChromName(struct annoStreamVcf *self, char *vcfChrom) /* We tolerate chr-less chrom names in VCF and BAM ("1" for "chr1" etc); to avoid * confusing the rest of the system, return the chr-ful version if it exists. */ { char *name = hashFindVal(self->chromNameHash, vcfChrom); if (name == NULL) { name = vcfChrom; struct twoBitFile *tbf = self->streamer.assembly->tbf; char buf[256]; if (! twoBitIsSequence(tbf, vcfChrom)) { safef(buf, sizeof(buf), "chr%s", vcfChrom); if (twoBitIsSequence(tbf, buf)) name = buf; } name = lmCloneString(self->chromNameHash->lm, name); hashAdd(self->chromNameHash, vcfChrom, name); } return name; } static char **nextRowUnfiltered(struct annoStreamVcf *self, char *minChrom, uint minEnd) /* Get the next VCF record and put the row text into autoSql words. * Return pointer to self->asWords if we get a row, otherwise NULL. */ { struct annoStreamer *sSelf = (struct annoStreamer *)self; char *regionChrom = sSelf->chrom; uint regionStart = sSelf->regionStart; uint regionEnd = sSelf->regionEnd; if (minChrom != NULL) { if (regionChrom == NULL) { regionChrom = minChrom; regionStart = minEnd; regionEnd = annoAssemblySeqSize(sSelf->assembly, minChrom); } else { regionStart = max(regionStart, minEnd); } } char **words = nextRowRaw(self); if (regionChrom != NULL && words != NULL) { if (self->isTabix && strcmp(getProperChromName(self, words[0]), regionChrom) < 0) lineFileSetTabixRegion(self->vcff->lf, regionChrom, regionStart, regionEnd); while (words != NULL && (strcmp(getProperChromName(self, words[0]), regionChrom) < 0 || - (sameString(words[0], regionChrom) && self->record->chromEnd < regionEnd))) + (sameString(words[0], regionChrom) && self->record->chromEnd < regionStart))) words = nextRowRaw(self); } return words; } static struct annoRow *asvNextRow(struct annoStreamer *sSelf, char *minChrom, uint minEnd, struct lm *callerLm) /* Return an annoRow encoding the next VCF record, or NULL if there are no more items. */ { struct annoStreamVcf *self = (struct annoStreamVcf *)sSelf; if (minChrom != NULL && sSelf->chrom != NULL && differentString(minChrom, sSelf->chrom)) errAbort("annoStreamVcf %s: nextRow minChrom='%s' but region chrom='%s'", sSelf->name, minChrom, sSelf->chrom); if (self->maxRecords > 0 && self->recordCount >= self->maxRecords) return NULL; char **words = nextRowUnfiltered(self, minChrom, minEnd); if (words == NULL) return NULL; // Skip past any left-join failures until we get a right-join failure, a passing row, or EOF. boolean rightFail = FALSE; while (annoFilterRowFails(sSelf->filters, words, self->numCols, &rightFail)) { if (rightFail) break; words = nextRowUnfiltered(self, minChrom, minEnd); if (words == NULL) return NULL; } struct vcfRecord *rec = self->record; vcfRecordTrimIndelLeftBase(rec); char *chrom = getProperChromName(self, rec->chrom); self->recordCount++; return annoRowFromStringArray(chrom, rec->chromStart, rec->chromEnd, rightFail, words, self->numCols, callerLm); } static void asvClose(struct annoStreamer **pVSelf) /* Close VCF file and free self. */ { if (pVSelf == NULL) return; struct annoStreamVcf *self = *(struct annoStreamVcf **)pVSelf; vcfFileFree(&(self->vcff)); // Don't free self->record -- currently it belongs to vcff's localMem dyStringFree(&(self->dyGt)); annoStreamerFree(pVSelf); } struct annoStreamer *annoStreamVcfNew(char *fileOrUrl, boolean isTabix, struct annoAssembly *aa, int maxRecords) /* Create an annoStreamer (subclass) object from a VCF file, which may * or may not have been compressed and indexed by tabix. */ { int maxErr = -1; // don't errAbort on VCF format warnings/errs struct vcfFile *vcff; if (isTabix) vcff = vcfTabixFileMayOpen(fileOrUrl, NULL, 0, 0, maxErr, 0); else vcff = vcfFileMayOpen(fileOrUrl, maxErr, 0, FALSE); if (vcff == NULL) errAbort("annoStreamVcfNew: unable to open VCF: '%s'", fileOrUrl); struct annoStreamVcf *self; AllocVar(self); struct annoStreamer *streamer = &(self->streamer); struct asObject *asObj = vcfAsObj(); annoStreamerInit(streamer, aa, asObj, fileOrUrl); streamer->rowType = arWords; streamer->setRegion = asvSetRegion; streamer->getHeader = asvGetHeader; streamer->nextRow = asvNextRow; streamer->close = asvClose; self->vcff = vcff; self->dyGt = dyStringNew(1024); self->chromNameHash = hashNew(0); self->isTabix = isTabix; self->numCols = slCount(asObj->columnList); self->numFileCols = 8; if (vcff->genotypeCount > 0) self->numFileCols = 9 + vcff->genotypeCount; self->maxRecords = maxRecords; return (struct annoStreamer *)self; }