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);
}
}
struct crTreeFile *crTreeFileOpen(char *fileName)
/* Open up r-tree index file - reading headers and verifying things. */
{
/* Open file and allocate structure to hold info from header etc. */
struct udcFile *udc = udcFileOpen(fileName, udcDefaultDir());
struct crTreeFile *crt = needMem(sizeof(*crt));
fileName = crt->fileName = cloneString(fileName);
crt->udc = udc;
/* 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;
udcMustReadOne(udc, magic);
if (magic != crTreeSig)
{
magic = byteSwap32(magic);
isSwapped = crt->isSwapped = TRUE;
if (magic != crTreeSig)
errAbort("%s is not a chromosome r-tree index file", fileName);
}
/* Read rest of high level header including notably the offsets to the
* chromosome and range indexes. */
bits32 reserved32;
udcMustReadOne(udc, reserved32);
crt->chromOffset = udcReadBits64(udc, isSwapped);
crt->cirOffset = udcReadBits64(udc, isSwapped);
/* Read in the chromosome index header. */
udcSeek(udc, crt->chromOffset);
crt->chromBpt = bptFileAttach(fileName, udc);
/* Read in range index header. */
udcSeek(udc, crt->cirOffset);
crt->cir = cirTreeFileAttach(fileName, udc);
return crt;
}
struct cirTreeFile *cirTreeFileOpen(char *fileName)
/* Open up r-tree index file - reading header and verifying things. */
{
return cirTreeFileAttach(cloneString(fileName), udcFileOpen(fileName, udcDefaultDir()));
}
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;
}
