void rt1dFindOld(char *tabFile, char *treeFile, bits32 chromIx, bits32 start, bits32 end)
/* rt1dCreate - find items in 1-D range tree. */
{
struct lineFile *lf = lineFileOpen(tabFile, TRUE);
struct cirTreeFile *crf = cirTreeFileOpen(treeFile);
struct fileOffsetSize *block, *blockList = cirTreeFindOverlappingBlocks(crf, chromIx, start, end);
uglyf("Got %d overlapping blocks\n", slCount(blockList));
for (block = blockList; block != NULL; block = block->next)
{
uglyf("block->offset %llu, block->size %llu\n", block->offset, block->size);
lineFileSeek(lf, block->offset, SEEK_SET);
bits64 sizeUsed = 0;
while (sizeUsed < block->size)
{
char *line;
int size;
if (!lineFileNext(lf, &line, &size))
errAbort("Couldn't read %s\n", lf->fileName);
char *parsedLine = cloneString(line);
char *row[3];
if (chopLine(parsedLine, row) != ArraySize(row))
errAbort("Badly formatted line of %s\n%s", lf->fileName, line);
bits32 bedChromIx = sqlUnsigned(row[0]);
bits32 bedStart = sqlUnsigned(row[1]);
bits32 bedEnd = sqlUnsigned(row[2]);
if (bedChromIx == chromIx && rangeIntersection(bedStart, bedEnd, start, end) > 0)
fprintf(stdout, "%s\n", line);
freeMem(parsedLine);
sizeUsed += size;
}
}
}
struct fileOffsetSize *crTreeFindOverlappingBlocks(struct crTreeFile *crt,
char *chrom, bits32 start, bits32 end)
/* Return list of file blocks that between them contain all items that overlap
* start/end on chromIx. Also there will be likely some non-overlapping items
* in these blocks too. When done, use slListFree to dispose of the result. */
{
/* Find chromosome index. Return NULL if no such chromosome*/
bits32 chromIx;
if (!bptFileFind(crt->chromBpt, chrom, strlen(chrom), &chromIx, sizeof(chromIx)))
return NULL;
return cirTreeFindOverlappingBlocks(crt->cir, chromIx, start, end);
}
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;
if (bbi->isSwapped)
idSize.chromId = byteSwap32(idSize.chromId);
if (retChromId != NULL)
*retChromId = idSize.chromId;
return cirTreeFindOverlappingBlocks(ctf, idSize.chromId, start, end);
}
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;
}
