src/lib/bwgQuery.c 1.18
1.18 2009/02/10 22:09:37 kent
Removing unused code.
Index: src/lib/bwgQuery.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/lib/bwgQuery.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -b -B -U 1000000 -r1.17 -r1.18
--- src/lib/bwgQuery.c 9 Feb 2009 02:43:23 -0000 1.17
+++ src/lib/bwgQuery.c 10 Feb 2009 22:09:37 -0000 1.18
@@ -1,372 +1,266 @@
/* bwgQuery - implements the query side of bigWig. See bwgInternal.h for definition of file
* format. */
#include "common.h"
#include "linefile.h"
#include "hash.h"
#include "localmem.h"
#include "options.h"
#include "sig.h"
#include "sqlNum.h"
#include "obscure.h"
#include "dystring.h"
#include "bPlusTree.h"
#include "cirTree.h"
#include "rangeTree.h"
#include "udc.h"
#include "bbiFile.h"
#include "bwgInternal.h"
#include "bigWig.h"
#include "bigBed.h"
static char const rcsid[] = "$Id$";
struct bbiFile *bigWigFileOpen(char *fileName)
/* Open up big wig file. */
{
return bbiFileOpen(fileName, bigWigSig, "big wig");
}
struct bwgSectionHead
/* A header from a bigWig file section */
{
bits32 chromId; /* Chromosome short identifier. */
bits32 start,end; /* Range covered. */
bits32 itemStep; /* For some section types, the # of bases between items. */
bits32 itemSpan; /* For some section types, the # of bases in each item. */
UBYTE type; /* Type byte. */
UBYTE reserved; /* Always zero for now. */
bits16 itemCount; /* Number of items in block. */
};
void bwgSectionHeadRead(struct bbiFile *bwf, struct bwgSectionHead *head)
/* Read section header. */
{
struct udcFile *udc = bwf->udc;
boolean isSwapped = bwf->isSwapped;
head->chromId = udcReadBits32(udc, isSwapped);
head->start = udcReadBits32(udc, isSwapped);
head->end = udcReadBits32(udc, isSwapped);
head->itemStep = udcReadBits32(udc, isSwapped);
head->itemSpan = udcReadBits32(udc, isSwapped);
head->type = udcGetChar(udc);
head->reserved = udcGetChar(udc);
head->itemCount = udcReadBits16(udc, isSwapped);
}
void bwgSectionHeadFromMem(char **pPt, struct bwgSectionHead *head, boolean isSwapped)
/* Read section header. */
{
char *pt = *pPt;
head->chromId = memReadBits32(&pt, isSwapped);
head->start = memReadBits32(&pt, isSwapped);
head->end = memReadBits32(&pt, isSwapped);
head->itemStep = memReadBits32(&pt, isSwapped);
head->itemSpan = memReadBits32(&pt, isSwapped);
head->type = *pt++;
head->reserved = *pt++;
head->itemCount = memReadBits16(&pt, isSwapped);
*pPt = pt;
}
void bigWigBlockDump(struct bbiFile *bwf, char *chrom, FILE *out)
/* Print out info on block starting at current position. */
{
boolean isSwapped = bwf->isSwapped;
struct udcFile *udc = bwf->udc;
struct bwgSectionHead head;
bwgSectionHeadRead(bwf, &head);
bits16 i;
float val;
switch (head.type)
{
case bwgTypeBedGraph:
{
fprintf(out, "#bedGraph section %s:%u-%u\n", chrom, head.start, head.end);
for (i=0; i<head.itemCount; ++i)
{
bits32 start = udcReadBits32(udc, isSwapped);
bits32 end = udcReadBits32(udc, isSwapped);
udcMustReadOne(udc, val);
fprintf(out, "%s\t%u\t%u\t%g\n", chrom, start, end, val);
}
break;
}
case bwgTypeVariableStep:
{
fprintf(out, "variableStep chrom=%s span=%u\n", chrom, head.itemSpan);
for (i=0; i<head.itemCount; ++i)
{
bits32 start = udcReadBits32(udc, isSwapped);
udcMustReadOne(udc, val);
fprintf(out, "%u\t%g\n", start+1, val);
}
break;
}
case bwgTypeFixedStep:
{
fprintf(out, "fixedStep chrom=%s start=%u step=%u span=%u\n",
chrom, head.start, head.itemStep, head.itemSpan);
for (i=0; i<head.itemCount; ++i)
{
udcMustReadOne(udc, val);
fprintf(out, "%g\n", val);
}
break;
}
default:
internalErr();
break;
}
}
-#ifdef DEBUG
-#endif /* DEBUG */
-#ifdef OLD
-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;
-struct udcFile *udc = bwf->udc;
-boolean isSwapped = bwf->isSwapped;
-float val;
-int i;
-
-// slSort(&blockList, fileOffsetSizeCmp);
-struct fileOffsetSize *mergedBlocks = fileOffsetSizeMerge(blockList);
-for (block = blockList; block != NULL; block = block->next)
- {
- udcSeek(udc, block->offset);
- bits64 endBlock = block->offset + block->size;
- while (udcTell(udc) < endBlock)
- {
- struct bwgSectionHead head;
- bwgSectionHeadRead(bwf, &head);
- switch (head.type)
- {
- case bwgTypeBedGraph:
- {
- for (i=0; i<head.itemCount; ++i)
- {
- bits32 s = udcReadBits32(udc, isSwapped);
- bits32 e = udcReadBits32(udc, isSwapped);
- udcMustReadOne(udc, val);
- 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 = udcReadBits32(udc, isSwapped);
- bits32 e = s + head.itemSpan;
- udcMustReadOne(udc, val);
- 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)
- {
- udcMustReadOne(udc, val);
- 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;
- }
- }
- }
-slFreeList(&mergedList);
-slFreeList(&blockList);
-slReverse(&list);
-return list;
-}
-#endif /* OLD */
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;
struct udcFile *udc = bwf->udc;
boolean isSwapped = bwf->isSwapped;
float val;
int i;
// slSort(&blockList, fileOffsetSizeCmp);
struct fileOffsetSize *mergedBlocks = fileOffsetSizeMerge(blockList);
for (block = mergedBlocks; block != NULL; block = block->next)
{
udcSeek(udc, block->offset);
char *blockBuf = needLargeMem(block->size);
udcRead(udc, blockBuf, block->size);
char *blockPt = blockBuf, *blockEnd = blockBuf + block->size;
while (blockPt < blockEnd)
{
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);
memReadOne(&blockPt, val);
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;
memReadOne(&blockPt, val);
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)
{
memReadOne(&blockPt, val);
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;
}
}
}
slFreeList(&mergedBlocks);
slFreeList(&blockList);
slReverse(&list);
return list;
}
boolean bigWigSummaryArray(char *fileName, char *chrom, bits32 start, bits32 end,
enum bbiSummaryType summaryType, int summarySize, double *summaryValues)
/* Fill in summaryValues with data from indicated chromosome range in bigWig file.
* Be sure to initialize summaryValues to a default value, which will not be touched
* for regions without data in file. (Generally you want the default value to either
* be 0.0 or nan("") depending on the application.) Returns FALSE if no data
* at that position. */
{
struct bbiFile *bwf = bigWigFileOpen(fileName);
boolean ret = bbiSummaryArray(bwf, chrom, start, end, bigWigIntervalQuery,
summaryType, summarySize, summaryValues);
bbiFileClose(&bwf);
return ret;
}
boolean bigWigSummaryArrayExtended(char *fileName, char *chrom, bits32 start, bits32 end,
int summarySize, struct bbiSummaryElement *summary)
/* Get extended summary information for summarySize evenely spaced elements into
* the summary array. */
{
struct bbiFile *bbi = bigWigFileOpen(fileName);
boolean ret = bbiSummaryArrayExtended(bbi, chrom, start, end, bigWigIntervalQuery,
summarySize, summary);
bbiFileClose(&bbi);
return ret;
}
double bigWigSingleSummary(char *fileName, char *chrom, int start, int end,
enum bbiSummaryType summaryType, double defaultVal)
/* Return the summarized single value for a range. */
{
double arrayOfOne = defaultVal;
bigWigSummaryArray(fileName, chrom, start, end, summaryType, 1, &arrayOfOne);
return arrayOfOne;
}