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;
struct udcFile *udc = bwf->udc;
int printCount = 0;
for (block = blockList; block != NULL; block = block->next)
{
udcSeek(udc, block->offset);
int oneCount = bigWigBlockDumpIntersectingRange(bwf, chrom, start, end, maxCount, out);
printCount += oneCount;
if (maxCount != 0)
{
if (oneCount >= maxCount)
break;
maxCount -= oneCount;
}
}
slFreeList(&blockList);
return printCount;
}
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;
}
void bigWigBlockDump(struct bbiFile *bwf, char *chrom, FILE *out)
/* Print out info on block starting at current position. */
{
bigWigBlockDumpIntersectingRange(bwf, chrom, 0, BIGNUM, 0, out);
}
