void cirTreeFileClose(struct cirTreeFile **pCrt) /* Close and free up cirTree file opened with cirTreeFileAttach. */ { struct cirTreeFile *crt = *pCrt; if (crt != NULL) { freez(&crt->fileName); udcFileClose(&crt->udc); cirTreeFileDetach(pCrt); } }
void crTreeFileClose(struct crTreeFile **pCrt) /* Close and free up crTree file opened with crTreeFileAttach. */ { struct crTreeFile *crt = *pCrt; if (crt != NULL) { cirTreeFileDetach(&crt->cir); bptFileDetach(&crt->chromBpt); udcFileClose(&crt->udc); freez(&crt->fileName); freez(pCrt); } }
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 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); 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; }