cb217f20b4a701edfa88f4db623266a9bf25202e kent Mon Mar 4 22:58:07 2013 -0800 Some more steps towards supporting multiple extra indexes in bigBed files. diff --git src/lib/bbiRead.c src/lib/bbiRead.c index f8bb53c..af27dd4 100644 --- src/lib/bbiRead.c +++ src/lib/bbiRead.c @@ -1,777 +1,783 @@ /* bbiRead - Big Binary Indexed file. Stuff that's common between bigWig and bigBed on the * read side. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "obscure.h" #include "zlibFace.h" #include "bPlusTree.h" #include "hmmstats.h" #include "cirTree.h" #include "udc.h" #include "bbiFile.h" struct bbiZoomLevel *bbiBestZoom(struct bbiZoomLevel *levelList, int desiredReduction) /* Return zoom level that is the closest one that is less than or equal to * desiredReduction. */ { if (desiredReduction < 0) errAbort("bad value %d for desiredReduction in bbiBestZoom", desiredReduction); if (desiredReduction <= 1) return NULL; int closestDiff = BIGNUM; struct bbiZoomLevel *closestLevel = NULL; struct bbiZoomLevel *level; for (level = levelList; level != NULL; level = level->next) { int diff = desiredReduction - level->reductionLevel; if (diff >= 0 && diff < closestDiff) { closestDiff = diff; closestLevel = level; } } return closestLevel; } boolean bbiFileCheckSigs(char *fileName, bits32 sig, char *typeName) /* check file signatures at beginning and end of file */ { int fd = mustOpenFd(fileName, O_RDONLY); bits32 magic; boolean isSwapped = FALSE; // look for signature at the beginning of the file mustReadFd(fd, &magic, sizeof(magic)); if (magic != sig) { magic = byteSwap32(magic); isSwapped = TRUE; if (magic != sig) return FALSE; } // look for signature at the end of the file mustLseek(fd, -sizeof(magic), SEEK_END); mustReadFd(fd, &magic, sizeof(magic)); mustCloseFd(&fd); if (isSwapped) { magic = byteSwap32(magic); if (magic != sig) return FALSE; } else { if (magic != sig) return FALSE; } return TRUE; } struct bbiFile *bbiFileOpen(char *fileName, bits32 sig, char *typeName) /* Open up big wig or big bed file. */ { /* This code needs to agree with code in two other places currently - bigBedFileCreate, * and bigWigFileCreate. I'm thinking of refactoring to share at least between * bigBedFileCreate and bigWigFileCreate. It'd be great so it could be structured * so that it could send the input in one chromosome at a time, and send in the zoom * stuff only after all the chromosomes are done. This'd potentially reduce the memory * footprint by a factor of 2 or 4. Still, for now it works. -JK */ struct bbiFile *bbi; AllocVar(bbi); bbi->fileName = cloneString(fileName); struct udcFile *udc = bbi->udc = udcFileOpen(fileName, udcDefaultDir()); /* Read magic number at head of file and use it to see if we are proper file type, and * see if we are byte-swapped. */ bits32 magic; boolean isSwapped = FALSE; udcMustRead(udc, &magic, sizeof(magic)); if (magic != sig) { magic = byteSwap32(magic); isSwapped = TRUE; if (magic != sig) errAbort("%s is not a %s file", fileName, typeName); } bbi->typeSig = sig; bbi->isSwapped = isSwapped; /* Read rest of defined bits of header, byte swapping as needed. */ bbi->version = udcReadBits16(udc, isSwapped); bbi->zoomLevels = udcReadBits16(udc, isSwapped); bbi->chromTreeOffset = udcReadBits64(udc, isSwapped); bbi->unzoomedDataOffset = udcReadBits64(udc, isSwapped); bbi->unzoomedIndexOffset = udcReadBits64(udc, isSwapped); bbi->fieldCount = udcReadBits16(udc, isSwapped); bbi->definedFieldCount = udcReadBits16(udc, isSwapped); bbi->asOffset = udcReadBits64(udc, isSwapped); bbi->totalSummaryOffset = udcReadBits64(udc, isSwapped); bbi->uncompressBufSize = udcReadBits32(udc, isSwapped); -bbi->nameIndexOffset = udcReadBits64(udc, isSwapped); - -/* Skip over reserved area. */ -udcSeek(udc, 64); // Absolute seek over fixed size 64 bit header +bbi->extensionOffset = udcReadBits64(udc, isSwapped); /* Read zoom headers. */ int i; struct bbiZoomLevel *level, *levelList = NULL; for (i=0; i<bbi->zoomLevels; ++i) { AllocVar(level); level->reductionLevel = udcReadBits32(udc, isSwapped); level->reserved = udcReadBits32(udc, isSwapped); level->dataOffset = udcReadBits64(udc, isSwapped); level->indexOffset = udcReadBits64(udc, isSwapped); slAddHead(&levelList, level); } slReverse(&levelList); bbi->levelList = levelList; +/* Deal with header extension if any. */ +if (bbi->extensionOffset != 0) + { + udcSeek(udc, bbi->extensionOffset); + bbi->extensionSize = udcReadBits16(udc, isSwapped); + bbi->extraIndexCount = udcReadBits16(udc, isSwapped); + bbi->extraIndexListOffset = udcReadBits64(udc, isSwapped); + } + /* Attach B+ tree of chromosome names and ids. */ udcSeek(udc, bbi->chromTreeOffset); bbi->chromBpt = bptFileAttach(fileName, udc); return bbi; } void bbiFileClose(struct bbiFile **pBwf) /* Close down a big wig/big bed file. */ { struct bbiFile *bwf = *pBwf; if (bwf != NULL) { cirTreeFileDetach(&bwf->unzoomedCir); slFreeList(&bwf->levelList); slFreeList(&bwf->levelList); bptFileDetach(&bwf->chromBpt); udcFileClose(&bwf->udc); freeMem(bwf->fileName); freez(pBwf); } } static void chromIdSizeHandleSwapped(boolean isSwapped, struct bbiChromIdSize *idSize) /* Swap bytes in chromosome Id and Size as needed. */ { if (isSwapped) { idSize->chromId = byteSwap32(idSize->chromId); idSize->chromSize = byteSwap32(idSize->chromSize); } } struct fileOffsetSize *bbiOverlappingBlocks(struct bbiFile *bbi, struct cirTreeFile *ctf, char *chrom, bits32 start, bits32 end, bits32 *retChromId) /* Fetch list of file blocks that contain items overlapping chromosome range. */ { struct bbiChromIdSize idSize; if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize))) return NULL; chromIdSizeHandleSwapped(bbi->isSwapped, &idSize); if (retChromId != NULL) *retChromId = idSize.chromId; return cirTreeFindOverlappingBlocks(ctf, idSize.chromId, start, end); } struct chromNameCallbackContext /* Some stuff that the bPlusTree traverser needs for context. */ { struct bbiChromInfo *list; /* The list we are building. */ boolean isSwapped; /* Need to byte-swap things? */ }; static void chromNameCallback(void *context, void *key, int keySize, void *val, int valSize) /* Callback that captures chromInfo from bPlusTree. */ { struct chromNameCallbackContext *c = context; struct bbiChromInfo *info; struct bbiChromIdSize *idSize = val; assert(valSize == sizeof(*idSize)); chromIdSizeHandleSwapped(c->isSwapped, idSize); AllocVar(info); info->name = cloneStringZ(key, keySize); info->id = idSize->chromId; info->size = idSize->chromSize; slAddHead(&c->list, info); } struct bbiChromInfo *bbiChromList(struct bbiFile *bbi) /* Return list of chromosomes. */ { struct chromNameCallbackContext context; context.list = NULL; context.isSwapped = bbi->isSwapped; bptFileTraverse(bbi->chromBpt, &context, chromNameCallback); slReverse(&context.list); return context.list; } bits32 bbiChromSize(struct bbiFile *bbi, char *chrom) /* Return chromosome size, or 0 if no such chromosome in file. */ { struct bbiChromIdSize idSize; if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize))) return 0; chromIdSizeHandleSwapped(bbi->isSwapped, &idSize); return idSize.chromSize; } void bbiChromInfoFree(struct bbiChromInfo **pInfo) /* Free up one chromInfo */ { struct bbiChromInfo *info = *pInfo; if (info != NULL) { freeMem(info->name); freez(pInfo); } } void bbiChromInfoFreeList(struct bbiChromInfo **pList) /* Free a list of dynamically allocated bbiChromInfo's */ { struct bbiChromInfo *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; bbiChromInfoFree(&el); } *pList = NULL; } void bbiAttachUnzoomedCir(struct bbiFile *bbi) /* Make sure unzoomed cir is attached. */ { if (bbi->unzoomedCir == NULL) { udcSeek(bbi->udc, bbi->unzoomedIndexOffset); bbi->unzoomedCir = cirTreeFileAttach(bbi->fileName, bbi->udc); } } enum bbiSummaryType bbiSummaryTypeFromString(char *string) /* Return summary type given a descriptive string. */ { if (sameWord(string, "mean") || sameWord(string, "average")) return bbiSumMean; else if (sameWord(string, "max") || sameWord(string, "maximum")) return bbiSumMax; else if (sameWord(string, "min") || sameWord(string, "minimum")) return bbiSumMin; else if (sameWord(string, "coverage") || sameWord(string, "dataCoverage")) return bbiSumCoverage; else if (sameWord(string, "std")) return bbiSumStandardDeviation; else { errAbort("Unknown bbiSummaryType %s", string); return bbiSumMean; /* Keep compiler quiet. */ } } char *bbiSummaryTypeToString(enum bbiSummaryType type) /* Convert summary type from enum to string representation. */ { switch (type) { case bbiSumMean: return "mean"; case bbiSumMax: return "max"; case bbiSumMin: return "min"; case bbiSumCoverage: return "coverage"; case bbiSumStandardDeviation: return "std"; default: errAbort("Unknown bbiSummaryType %d", (int)type); return NULL; } } #ifdef UNUSED static void bbiSummaryOnDiskRead(struct bbiFile *bbi, struct bbiSummaryOnDisk *sum) /* Read in summary from file. */ { struct udcFile *udc = bbi->udc; boolean isSwapped = bbi->isSwapped; sum->chromId = udcReadBits32(udc, isSwapped); sum->start = udcReadBits32(udc, isSwapped); sum->end = udcReadBits32(udc, isSwapped); sum->validCount = udcReadBits32(udc, isSwapped); // looks like a bug to me, these should call udcReadFloat() udcMustReadOne(udc, sum->minVal); udcMustReadOne(udc, sum->maxVal); udcMustReadOne(udc, sum->sumData); udcMustReadOne(udc, sum->sumSquares); } #endif /* UNUSED */ static void bbiSummaryHandleSwapped(struct bbiFile *bbi, struct bbiSummaryOnDisk *in) /* Swap integer fields in summary as needed. */ { if (bbi->isSwapped) { in->chromId = byteSwap32(in->chromId); in->start = byteSwap32(in->start); in->end = byteSwap32(in->end); in->validCount = byteSwap32(in->validCount); in->minVal = byteSwapFloat(in->minVal); in->maxVal = byteSwapFloat(in->maxVal); in->sumData = byteSwapFloat(in->sumData); in->sumSquares = byteSwapFloat(in->sumSquares); } } static struct bbiSummary *bbiSummaryFromOnDisk(struct bbiSummaryOnDisk *in) /* Create a bbiSummary unlinked to anything from input in onDisk format. */ { struct bbiSummary *out; AllocVar(out); out->chromId = in->chromId; out->start = in->start; out->end = in->end; out->validCount = in->validCount; out->minVal = in->minVal; out->maxVal = in->maxVal; out->sumData = in->sumData; out->sumSquares = in->sumSquares; return out; } struct bbiSummary *bbiSummariesInRegion(struct bbiZoomLevel *zoom, struct bbiFile *bbi, int chromId, bits32 start, bits32 end) /* Return list of all summaries in region at given zoom level of bbiFile. */ { struct bbiSummary *sumList = NULL, *sum; struct udcFile *udc = bbi->udc; udcSeek(udc, zoom->indexOffset); struct cirTreeFile *ctf = cirTreeFileAttach(bbi->fileName, bbi->udc); struct fileOffsetSize *blockList = cirTreeFindOverlappingBlocks(ctf, chromId, start, end); struct fileOffsetSize *block, *beforeGap, *afterGap; /* Set up for uncompression optionally. */ char *uncompressBuf = NULL; if (bbi->uncompressBufSize > 0) uncompressBuf = needLargeMem(bbi->uncompressBufSize); /* This loop is a little complicated because we merge the read requests for efficiency, but we * have to then go back through the data one unmerged block at a time. */ for (block = blockList; block != NULL; ) { /* Find contigious blocks and read them into mergedBuf. */ fileOffsetSizeFindGap(block, &beforeGap, &afterGap); bits64 mergedOffset = block->offset; bits64 mergedSize = beforeGap->offset + beforeGap->size - mergedOffset; udcSeek(udc, mergedOffset); char *mergedBuf = needLargeMem(mergedSize); udcMustRead(udc, mergedBuf, mergedSize); char *blockBuf = mergedBuf; /* Loop through individual blocks within merged section. */ for (;block != afterGap; block = block->next) { /* Uncompress if necessary. */ char *blockPt, *blockEnd; if (uncompressBuf) { blockPt = uncompressBuf; int uncSize = zUncompress(blockBuf, block->size, uncompressBuf, bbi->uncompressBufSize); blockEnd = blockPt + uncSize; } else { blockPt = blockBuf; blockEnd = blockPt + block->size; } /* Figure out bounds and number of items in block. */ int blockSize = blockEnd - blockPt; struct bbiSummaryOnDisk *dSum; int itemSize = sizeof(*dSum); assert(blockSize % itemSize == 0); int itemCount = blockSize / itemSize; /* Read in items and convert to memory list format. */ int i; for (i=0; i<itemCount; ++i) { dSum = (void *)blockPt; blockPt += sizeof(*dSum); bbiSummaryHandleSwapped(bbi, dSum); if (dSum->chromId == chromId) { int s = max(dSum->start, start); int e = min(dSum->end, end); if (s < e) { sum = bbiSummaryFromOnDisk(dSum); slAddHead(&sumList, sum); } } } assert(blockPt == blockEnd); blockBuf += block->size; } freeMem(mergedBuf); } freeMem(uncompressBuf); slFreeList(&blockList); cirTreeFileDetach(&ctf); slReverse(&sumList); return sumList; } static bits32 bbiSummarySlice(struct bbiFile *bbi, bits32 baseStart, bits32 baseEnd, struct bbiSummary *sumList, struct bbiSummaryElement *el) /* Update retVal with the average value if there is any data in interval. Return number * of valid data bases in interval. */ { bits32 validCount = 0; if (sumList != NULL) { double minVal = sumList->minVal; double maxVal = sumList->maxVal; double sumData = 0, sumSquares = 0; struct bbiSummary *sum; for (sum = sumList; sum != NULL && sum->start < baseEnd; sum = sum->next) { int overlap = rangeIntersection(baseStart, baseEnd, sum->start, sum->end); if (overlap > 0) { double overlapFactor = (double)overlap / (sum->end - sum->start); validCount += sum->validCount * overlapFactor; sumData += sum->sumData * overlapFactor; sumSquares += sum->sumSquares * overlapFactor; if (maxVal < sum->maxVal) maxVal = sum->maxVal; if (minVal > sum->minVal) minVal = sum->minVal; } } if (validCount > 0) { el->validCount = validCount; el->minVal = minVal; el->maxVal = maxVal; el->sumData = sumData; el->sumSquares = sumSquares; } } return validCount; } static int bbiChromId(struct bbiFile *bbi, char *chrom) /* Return chromosome Id */ { struct bbiChromIdSize idSize; if (!bptFileFind(bbi->chromBpt, chrom, strlen(chrom), &idSize, sizeof(idSize))) return -1; chromIdSizeHandleSwapped(bbi->isSwapped, &idSize); return idSize.chromId; } static boolean bbiSummaryArrayFromZoom(struct bbiZoomLevel *zoom, struct bbiFile *bbi, char *chrom, bits32 start, bits32 end, int summarySize, struct bbiSummaryElement *summary) /* Look up region in index and get data at given zoom level. Summarize this data * in the summary array. */ { boolean result = FALSE; int chromId = bbiChromId(bbi, chrom); if (chromId < 0) return FALSE; struct bbiSummary *sum, *sumList = bbiSummariesInRegion(zoom, bbi, chromId, start, end); if (sumList != NULL) { int i; bits32 baseStart = start, baseEnd; bits32 baseCount = end - start; sum = sumList; for (i=0; i<summarySize; ++i) { /* Calculate end of this part of summary */ baseEnd = start + (bits64)baseCount*(i+1)/summarySize; /* Advance sum to skip over parts we are no longer interested in. */ while (sum != NULL && sum->end <= baseStart) sum = sum->next; if (bbiSummarySlice(bbi, baseStart, baseEnd, sum, &summary[i])) result = TRUE; /* Next time round start where we left off. */ baseStart = baseEnd; } slFreeList(&sumList); } return result; } static bits32 bbiIntervalSlice(struct bbiFile *bbi, bits32 baseStart, bits32 baseEnd, struct bbiInterval *intervalList, struct bbiSummaryElement *el) /* Update retVal with the average value if there is any data in interval. Return number * of valid data bases in interval. */ { double validCount = 0; if (intervalList != NULL) { struct bbiInterval *interval; double sumData = 0, sumSquares = 0; double minVal = intervalList->val; double maxVal = intervalList->val; for (interval = intervalList; interval != NULL && interval->start < baseEnd; interval = interval->next) { int overlap = rangeIntersection(baseStart, baseEnd, interval->start, interval->end); if (overlap > 0) { int intervalSize = interval->end - interval->start; double overlapFactor = (double)overlap / intervalSize; double intervalWeight = intervalSize * overlapFactor; validCount += intervalWeight; sumData += interval->val * intervalWeight; sumSquares += interval->val * interval->val * intervalWeight; if (maxVal < interval->val) maxVal = interval->val; if (minVal > interval->val) minVal = interval->val; } } el->validCount = round(validCount); el->minVal = minVal; el->maxVal = maxVal; el->sumData = sumData; el->sumSquares = sumSquares; } return round(validCount); } static boolean bbiSummaryArrayFromFull(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end, BbiFetchIntervals fetchIntervals, int summarySize, struct bbiSummaryElement *summary) /* Summarize data, not using zoom. */ { struct bbiInterval *intervalList = NULL, *interval; struct lm *lm = lmInit(0); intervalList = (*fetchIntervals)(bbi, chrom, start, end, lm); boolean result = FALSE; if (intervalList != NULL); { int i; bits32 baseStart = start, baseEnd; bits32 baseCount = end - start; interval = intervalList; for (i=0; i<summarySize; ++i) { /* Calculate end of this part of summary */ baseEnd = start + (bits64)baseCount*(i+1)/summarySize; int end1 = baseEnd; if (end1 == baseStart) end1 = baseStart+1; /* Advance interval to skip over parts we are no longer interested in. */ while (interval != NULL && interval->end <= baseStart) interval = interval->next; if (bbiIntervalSlice(bbi, baseStart, end1, interval, &summary[i])) result = TRUE; /* Next time round start where we left off. */ baseStart = baseEnd; } } lmCleanup(&lm); return result; } boolean bbiSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end, BbiFetchIntervals fetchIntervals, int summarySize, struct bbiSummaryElement *summary) /* Fill in summary with data from indicated chromosome range in bigWig file. * Returns FALSE if no data at that position. */ { boolean result = FALSE; /* Protect from bad input. */ if (start >= end) return result; bzero(summary, summarySize * sizeof(summary[0])); /* Figure out what size of data we want. We actually want to get 2 data points per summary * value if possible to minimize the effect of a data point being split between summary pixels. */ bits32 baseSize = end - start; int fullReduction = (baseSize/summarySize); int zoomLevel = fullReduction/2; if (zoomLevel < 0) zoomLevel = 0; /* Get the closest zoom level less than what we're looking for. */ struct bbiZoomLevel *zoom = bbiBestZoom(bbi->levelList, zoomLevel); if (zoom != NULL) result = bbiSummaryArrayFromZoom(zoom, bbi, chrom, start, end, summarySize, summary); else result = bbiSummaryArrayFromFull(bbi, chrom, start, end, fetchIntervals, summarySize, summary); return result; } boolean bbiSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end, BbiFetchIntervals fetchIntervals, enum bbiSummaryType summaryType, int summarySize, double *summaryValues) /* Fill in summaryValues with data from indicated chromosome range in bigWig file. * Be sure to initialize summaryValues to a default value, which will not be touched * for regions without data in file. (Generally you want the default value to either * be 0.0 or nan("") depending on the application.) Returns FALSE if no data * at that position. */ { struct bbiSummaryElement *elements; AllocArray(elements, summarySize); boolean ret = bbiSummaryArrayExtended(bbi, chrom, start, end, fetchIntervals, summarySize, elements); if (ret) { int i; double covFactor = (double)summarySize/(end - start); for (i=0; i<summarySize; ++i) { struct bbiSummaryElement *el = &elements[i]; if (el->validCount > 0) { double val; switch (summaryType) { case bbiSumMean: val = el->sumData/el->validCount; break; case bbiSumMax: val = el->maxVal; break; case bbiSumMin: val = el->minVal; break; case bbiSumCoverage: val = covFactor*el->validCount; break; case bbiSumStandardDeviation: val = calcStdFromSums(el->sumData, el->sumSquares, el->validCount); break; default: internalErr(); val = 0.0; break; } summaryValues[i] = val; } } } freeMem(elements); return ret; } struct bbiSummaryElement bbiTotalSummary(struct bbiFile *bbi) /* Return summary of entire file! */ { struct udcFile *udc = bbi->udc; boolean isSwapped = bbi->isSwapped; struct bbiSummaryElement res; ZeroVar(&res); if (bbi->totalSummaryOffset != 0) { udcSeek(udc, bbi->totalSummaryOffset); res.validCount = udcReadBits64(udc, isSwapped); res.minVal = udcReadDouble(udc, isSwapped); res.maxVal = udcReadDouble(udc, isSwapped); res.sumData = udcReadDouble(udc, isSwapped); res.sumSquares = udcReadDouble(udc, isSwapped); } else if (bbi->version == 1) /* Require version 1 so as not to have to deal with compression. Should not happen * to have NULL totalSummaryOffset for non-empty version 2+ file anyway. */ { /* Find most extreme zoom. */ struct bbiZoomLevel *bestZoom = NULL, *zoom; bits32 bestReduction = 0; for (zoom = bbi->levelList; zoom != NULL; zoom = zoom->next) { if (zoom->reductionLevel > bestReduction) { bestReduction = zoom->reductionLevel; bestZoom = zoom; } } if (bestZoom != NULL) { udcSeek(udc, bestZoom->dataOffset); bits32 zoomSectionCount = udcReadBits32(udc, isSwapped); bits32 i; for (i=0; i<zoomSectionCount; ++i) { /* Read, but ignore, position. */ bits32 chromId, chromStart, chromEnd; chromId = udcReadBits32(udc, isSwapped); chromStart = udcReadBits32(udc, isSwapped); chromEnd = udcReadBits32(udc, isSwapped); /* First time through set values, rest of time add to them. */ if (i == 0) { res.validCount = udcReadBits32(udc, isSwapped); res.minVal = udcReadFloat(udc, isSwapped); res.maxVal = udcReadFloat(udc, isSwapped); res.sumData = udcReadFloat(udc, isSwapped); res.sumSquares = udcReadFloat(udc, isSwapped); } else { res.validCount += udcReadBits32(udc, isSwapped); float minVal = udcReadFloat(udc, isSwapped); if (minVal < res.minVal) res.minVal = minVal; float maxVal = udcReadFloat(udc, isSwapped); if (maxVal > res.maxVal) res.maxVal = maxVal; res.sumData += udcReadFloat(udc, isSwapped); res.sumSquares += udcReadFloat(udc, isSwapped); } } } } return res; } time_t bbiUpdateTime(struct bbiFile *bbi) /* return bbi->udc->updateTime */ { struct udcFile *udc = bbi->udc; return udcUpdateTime(udc); } char *bbiCachedChromLookup(struct bbiFile *bbi, int chromId, int lastChromId, char *chromBuf, int chromBufSize) /* Return chromosome name corresponding to chromId. Because this is a bit expensive, * if you are doing this repeatedly pass in the chromId used in the previous call to * this in lastChromId, which will save it from doing the lookup again on the same * chromosome. Pass in -1 to lastChromId if this is the first time or if you can't be * bothered. The chromBufSize should be at greater or equal to bbi->keySize+1. */ { if (chromId != lastChromId) bptStringKeyAtPos(bbi->chromBpt, chromId, chromBuf, chromBufSize); return chromBuf; }