static bool openBlock(BigFileReaderData * data, struct fileOffsetSize * block, char * blockBuf) {
size_t uncompressBufSize = data->bwf->uncompressBufSize;
if (uncompressBufSize > 0) {
int uncSize = zUncompress(blockBuf, block->size, data->uncompressBuf, uncompressBufSize);
data->blockEnd = data->uncompressBuf + uncSize;
} else {
data->uncompressBuf = blockBuf;
data->blockEnd = blockBuf + block->size;
}
// Callback to specialised BigBed or BigWig function
return data->readBuffer(data);
}
int bigWigIntervalDump(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end, int maxCount,
FILE *out)
/* Print out info on bigWig parts that intersect chrom:start-end. Set maxCount to 0 if you
* don't care how many are printed. Returns number printed. */
{
if (bwf->typeSig != bigWigSig)
errAbort("Trying to do bigWigIntervalDump on a non big-wig file.");
bbiAttachUnzoomedCir(bwf);
struct fileOffsetSize *blockList = bbiOverlappingBlocks(bwf, bwf->unzoomedCir,
chrom, start, end, NULL);
struct fileOffsetSize *block, *beforeGap, *afterGap;
struct udcFile *udc = bwf->udc;
int printCount = 0;
/* Set up for uncompression optionally. */
char *uncompressBuf = NULL;
if (bwf->uncompressBufSize > 0)
uncompressBuf = needLargeMem(bwf->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, bwf->uncompressBufSize);
blockEnd = blockPt + uncSize;
}
else
{
blockPt = blockBuf;
blockEnd = blockPt + block->size;
}
/* Do the actual dump. */
int oneCount = bigWigBlockDumpIntersectingRange(bwf->isSwapped, blockPt, blockEnd,
chrom, start, end, maxCount, out);
/* Keep track of how many dumped, not exceeding maximum. */
printCount += oneCount;
if (maxCount != 0)
{
if (oneCount >= maxCount)
break;
maxCount -= oneCount;
}
blockBuf += block->size;
}
freeMem(mergedBuf);
}
freeMem(uncompressBuf);
slFreeList(&blockList);
return printCount;
}
struct bbiInterval *bigWigIntervalQuery(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
struct lm *lm)
/* Get data for interval. Return list allocated out of lm. */
{
if (bwf->typeSig != bigWigSig)
errAbort("Trying to do bigWigIntervalQuery on a non big-wig file.");
bbiAttachUnzoomedCir(bwf);
struct bbiInterval *el, *list = NULL;
struct fileOffsetSize *blockList = bbiOverlappingBlocks(bwf, bwf->unzoomedCir,
chrom, start, end, NULL);
struct fileOffsetSize *block, *beforeGap, *afterGap;
struct udcFile *udc = bwf->udc;
boolean isSwapped = bwf->isSwapped;
float val;
int i;
/* Set up for uncompression optionally. */
char *uncompressBuf = NULL;
if (bwf->uncompressBufSize > 0)
uncompressBuf = needLargeMem(bwf->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, bwf->uncompressBufSize);
blockEnd = blockPt + uncSize;
}
else
{
blockPt = blockBuf;
blockEnd = blockPt + block->size;
}
/* Deal with insides of block. */
struct bwgSectionHead head;
bwgSectionHeadFromMem(&blockPt, &head, isSwapped);
switch (head.type)
{
case bwgTypeBedGraph:
{
for (i=0; i<head.itemCount; ++i)
{
bits32 s = memReadBits32(&blockPt, isSwapped);
bits32 e = memReadBits32(&blockPt, isSwapped);
val = memReadFloat(&blockPt, isSwapped);
if (s < start) s = start;
if (e > end) e = end;
if (s < e)
{
lmAllocVar(lm, el);
el->start = s;
el->end = e;
el->val = val;
slAddHead(&list, el);
}
}
break;
}
case bwgTypeVariableStep:
{
for (i=0; i<head.itemCount; ++i)
{
bits32 s = memReadBits32(&blockPt, isSwapped);
bits32 e = s + head.itemSpan;
val = memReadFloat(&blockPt, isSwapped);
if (s < start) s = start;
if (e > end) e = end;
if (s < e)
{
lmAllocVar(lm, el);
el->start = s;
el->end = e;
el->val = val;
slAddHead(&list, el);
}
}
break;
}
case bwgTypeFixedStep:
{
bits32 s = head.start;
bits32 e = s + head.itemSpan;
for (i=0; i<head.itemCount; ++i)
{
val = memReadFloat(&blockPt, isSwapped);
bits32 clippedS = s, clippedE = e;
if (clippedS < start) clippedS = start;
if (clippedE > end) clippedE = end;
if (clippedS < clippedE)
{
lmAllocVar(lm, el);
el->start = clippedS;
el->end = clippedE;
el->val = val;
slAddHead(&list, el);
}
s += head.itemStep;
e += head.itemStep;
}
break;
}
default:
internalErr();
break;
}
assert(blockPt == blockEnd);
blockBuf += block->size;
}
freeMem(mergedBuf);
}
freeMem(uncompressBuf);
slFreeList(&blockList);
slReverse(&list);
return list;
}
static void fetchIntoBuf(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
struct bigWigValsOnChrom *chromVals)
/* Get data for interval. Return list allocated out of lm. */
{
/* A lot of code duplicated with bigWigIntervalQuery, but here the clipping
* is simplified since always working across full chromosome, and the output is
* different. Since both of these are in inner loops and speed critical, it's hard
* to factor out without perhaps making it worse than the bit of duplication. */
if (bwf->typeSig != bigWigSig)
errAbort("Trying to do fetchIntoBuf on a non big-wig file.");
bbiAttachUnzoomedCir(bwf);
struct fileOffsetSize *blockList = bbiOverlappingBlocks(bwf, bwf->unzoomedCir,
chrom, start, end, NULL);
struct fileOffsetSize *block, *beforeGap, *afterGap;
struct udcFile *udc = bwf->udc;
boolean isSwapped = bwf->isSwapped;
float val;
int i;
Bits *covBuf = chromVals->covBuf;
double *valBuf = chromVals->valBuf;
/* Set up for uncompression optionally. */
char *uncompressBuf = NULL;
if (bwf->uncompressBufSize > 0)
uncompressBuf = needLargeMem(bwf->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, bwf->uncompressBufSize);
blockEnd = blockPt + uncSize;
}
else
{
blockPt = blockBuf;
blockEnd = blockPt + block->size;
}
/* Deal with insides of block. */
struct bwgSectionHead head;
bwgSectionHeadFromMem(&blockPt, &head, isSwapped);
switch (head.type)
{
case bwgTypeBedGraph:
{
for (i=0; i<head.itemCount; ++i)
{
bits32 s = memReadBits32(&blockPt, isSwapped);
bits32 e = memReadBits32(&blockPt, isSwapped);
bitSetRange(covBuf, s, e-s);
val = memReadFloat(&blockPt, isSwapped);
bits32 j;
for (j=s; j<e; ++j)
valBuf[j] = val;
}
break;
}
case bwgTypeVariableStep:
{
for (i=0; i<head.itemCount; ++i)
{
bits32 s = memReadBits32(&blockPt, isSwapped);
val = memReadFloat(&blockPt, isSwapped);
bitSetRange(covBuf, s, head.itemSpan);
bits32 e = s + head.itemSpan;
bits32 j;
for (j=s; j<e; ++j)
valBuf[j] = val;
}
break;
}
case bwgTypeFixedStep:
{
/* Do a little optimization for the most common and worst case - step1/span1 */
if (head.itemStep == 1 && head.itemSpan == 1)
{
bits32 s = head.start;
bits32 e = head.end;
bitSetRange(covBuf, s, e-s);
bits32 j;
for (j=s; j<e; ++j)
valBuf[j] = memReadFloat(&blockPt, isSwapped);
}
else
{
bits32 s = head.start;
bits32 e = s + head.itemSpan;
for (i=0; i<head.itemCount; ++i)
{
bitSetRange(covBuf, s, head.itemSpan);
val = memReadFloat(&blockPt, isSwapped);
bits32 j;
for (j=s; j<e; ++j)
valBuf[j] = val;
s += head.itemStep;
e += head.itemStep;
}
}
break;
}
default:
internalErr();
break;
}
assert(blockPt == blockEnd);
blockBuf += block->size;
}
freeMem(mergedBuf);
}
freeMem(uncompressBuf);
slFreeList(&blockList);
}
static struct bigBedInterval *bigBedIntervalsMatchingName(struct bbiFile *bbi,
struct fileOffsetSize *fosList, BbFirstWordMatch matcher, int fieldIx,
void *target, struct lm *lm)
/* Return list of intervals inside of sectors of bbiFile defined by fosList where the name
* matches target somehow. */
{
struct bigBedInterval *interval, *intervalList = NULL;
struct fileOffsetSize *fos;
boolean isSwapped = bbi->isSwapped;
for (fos = fosList; fos != NULL; fos = fos->next)
{
/* Read in raw data */
udcSeek(bbi->udc, fos->offset);
char *rawData = needLargeMem(fos->size);
udcRead(bbi->udc, rawData, fos->size);
/* Optionally uncompress data, and set data pointer to uncompressed version. */
char *uncompressedData = NULL;
char *data = NULL;
int dataSize = 0;
if (bbi->uncompressBufSize > 0)
{
data = uncompressedData = needLargeMem(bbi->uncompressBufSize);
dataSize = zUncompress(rawData, fos->size, uncompressedData, bbi->uncompressBufSize);
}
else
{
data = rawData;
dataSize = fos->size;
}
/* Set up for "memRead" routines to more or less treat memory block like file */
char *blockPt = data, *blockEnd = data + dataSize;
struct dyString *dy = dyStringNew(32); // Keep bits outside of chrom/start/end here
/* Read next record into local variables. */
while (blockPt < blockEnd)
{
bits32 chromIx = memReadBits32(&blockPt, isSwapped);
bits32 s = memReadBits32(&blockPt, isSwapped);
bits32 e = memReadBits32(&blockPt, isSwapped);
int c;
dyStringClear(dy);
// TODO - can simplify this probably just to for (;;) {if ((c = *blockPt++) == 0) ...
while ((c = *blockPt++) >= 0)
{
if (c == 0)
break;
dyStringAppendC(dy, c);
}
if ((*matcher)(dy->string, fieldIx, target))
{
lmAllocVar(lm, interval);
interval->start = s;
interval->end = e;
interval->rest = cloneString(dy->string);
interval->chromId = chromIx;
slAddHead(&intervalList, interval);
}
}
/* Clean up temporary buffers. */
dyStringFree(&dy);
freez(&uncompressedData);
freez(&rawData);
}
slReverse(&intervalList);
return intervalList;
}
struct bigBedInterval *bigBedIntervalQuery(struct bbiFile *bbi, char *chrom,
bits32 start, bits32 end, int maxItems, struct lm *lm)
/* Get data for interval. Return list allocated out of lm. Set maxItems to maximum
* number of items to return, or to 0 for all items. */
{
struct bigBedInterval *el, *list = NULL;
int itemCount = 0;
bbiAttachUnzoomedCir(bbi);
bits32 chromId;
struct fileOffsetSize *blockList = bbiOverlappingBlocks(bbi, bbi->unzoomedCir,
chrom, start, end, &chromId);
struct fileOffsetSize *block, *beforeGap, *afterGap;
struct udcFile *udc = bbi->udc;
boolean isSwapped = bbi->isSwapped;
struct dyString *dy = dyStringNew(32);
/* Set up for uncompression optionally. */
char *uncompressBuf = NULL;
if (bbi->uncompressBufSize > 0)
uncompressBuf = needLargeMem(bbi->uncompressBufSize);
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;
}
while (blockPt < blockEnd)
{
/* Read next record into local variables. */
bits32 chr = memReadBits32(&blockPt, isSwapped); // Read and discard chromId
bits32 s = memReadBits32(&blockPt, isSwapped);
bits32 e = memReadBits32(&blockPt, isSwapped);
int c;
dyStringClear(dy);
// TODO - can simplify this probably just to for (;;) {if ((c = *blockPt++) == 0) ...
while ((c = *blockPt++) >= 0)
{
if (c == 0)
break;
dyStringAppendC(dy, c);
}
/* If we're actually in range then copy it into a new element and add to list. */
if (chr == chromId && s < end && e > start)
{
++itemCount;
if (maxItems > 0 && itemCount > maxItems)
break;
lmAllocVar(lm, el);
el->start = s;
el->end = e;
if (dy->stringSize > 0)
el->rest = lmCloneString(lm, dy->string);
el->chromId = chromId;
slAddHead(&list, el);
}
}
if (maxItems > 0 && itemCount > maxItems)
break;
blockBuf += block->size;
}
if (maxItems > 0 && itemCount > maxItems)
break;
freez(&mergedBuf);
}
freeMem(uncompressBuf);
dyStringFree(&dy);
slFreeList(&blockList);
slReverse(&list);
return list;
}
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;
}
