static void addBwCorrelations(struct bbiChromInfo *chrom, struct genomeRangeTree *targetGrt,
struct bigWigValsOnChrom *aVals, struct bigWigValsOnChrom *bVals,
struct bbiFile *aBbi, struct bbiFile *bBbi,
double aThreshold, double bThreshold,
struct correlate *c, struct correlate *cInEnriched, struct correlate *cClipped)
/* Find bits of a and b that overlap and also overlap with targetRanges. Do correlations there */
{
struct rbTree *targetRanges = genomeRangeTreeFindRangeTree(targetGrt, chrom->name);
if (bigWigValsOnChromFetchData(aVals, chrom->name, aBbi) &&
bigWigValsOnChromFetchData(bVals, chrom->name, bBbi) )
{
double *a = aVals->valBuf, *b = bVals->valBuf;
int i, end = chrom->size;
for (i=0; i<end; ++i)
{
double aVal = a[i], bVal = b[i];
correlateNext(c, aVal, bVal);
if (aVal > aThreshold) aVal = aThreshold;
if (bVal > bThreshold) bVal = bThreshold;
correlateNext(cClipped, aVal, bVal);
}
if (targetRanges != NULL)
{
struct range *range, *rangeList = rangeTreeList(targetRanges);
for (range = rangeList; range != NULL; range = range->next)
{
int start = range->start, end = range->end;
for (i=start; i<end; ++i)
correlateNext(cInEnriched, a[i], b[i]);
}
}
}
}
void doItBigWig(struct inInfo *in, struct bed *chiaList, struct bigWigValsOnChrom *chromVals,
double *out1, double *out2)
{
struct bed *chromStart, *chromEnd, *chia;
int chiaIx = 0;
for (chromStart = chiaList; chromStart != NULL; chromStart = chromEnd)
{
chromEnd = bedListNextDifferentChrom(chromStart);
if (bigWigValsOnChromFetchData(chromVals, chromStart->chrom, in->bbi))
{
for (chia = chromStart; chia != chromEnd; chia = chia->next)
{
int blockStart = chia->chromStart;
int blockSize = chia->blockSizes[0];
out1[chiaIx] = averageInRegion(chromVals, blockStart, blockSize);
blockStart = chia->chromStart + chia->chromStarts[1];
blockSize = chia->blockSizes[1];
out2[chiaIx] = averageInRegion(chromVals, blockStart, blockSize);
++chiaIx;
}
}
else
{
/* No data on this chrom, just output zero everywhere. */
for (chia = chromStart; chia != chromEnd; chia = chia->next)
{
out1[chiaIx] = out2[chiaIx] = 0;
++chiaIx;
}
}
verboseDot();
}
}
void averageFetchingEachChrom(struct bbiFile *bbi, struct bed **pBedList, int fieldCount,
FILE *f, FILE *bedF)
/* Do the averaging by sorting bedList by chromosome, and then processing each chromosome
* at once. Faster for long bedLists. */
{
/* Sort by chromosome. */
slSort(pBedList, bedCmpChrom);
struct bigWigValsOnChrom *chromVals = bigWigValsOnChromNew();
struct bed *bed, *bedList, *nextChrom;
verbose(1, "processing chromosomes");
for (bedList = *pBedList; bedList != NULL; bedList = nextChrom)
{
/* Figure out which chromosome we're working on, and the last bed using it. */
char *chrom = bedList->chrom;
nextChrom = nextChromInList(bedList);
verbose(2, "Processing %s\n", chrom);
if (bigWigValsOnChromFetchData(chromVals, chrom, bbi))
{
double *valBuf = chromVals->valBuf;
Bits *covBuf = chromVals->covBuf;
/* Loop through beds doing sums and outputting. */
for (bed = bedList; bed != nextChrom; bed = bed->next)
{
int size = 0, coverage = 0;
double sum = 0.0;
if (sampleAroundCenter > 0)
{
int center = (bed->chromStart + bed->chromEnd)/2;
int left = center - (sampleAroundCenter/2);
addBufIntervalInfo(valBuf, covBuf, left, left+sampleAroundCenter,
&size, &coverage, &sum);
}
else
{
if (fieldCount < 12)
{
addBufIntervalInfo(valBuf, covBuf, bed->chromStart, bed->chromEnd,
&size, &coverage, &sum);
}
else
{
int i;
for (i=0; i<bed->blockCount; ++i)
{
int start = bed->chromStart + bed->chromStarts[i];
int end = start + bed->blockSizes[i];
addBufIntervalInfo(valBuf, covBuf, start, end, &size, &coverage, &sum);
}
}
}
/* Print out result, fudging mean to 0 if no coverage at all. */
double mean = 0;
if (coverage > 0)
mean = sum/coverage;
fprintf(f, "%s\t%d\t%d\t%g\t%g\t%g\n", bed->name, size, coverage, sum, sum/size, mean);
optionallyPrintBedPlus(bedF, bed, fieldCount, mean);
}
verboseDot();
}
else
{
/* If no bigWig data on this chromosome, just output as if coverage is 0 */
for (bed = bedList; bed != nextChrom; bed = bed->next)
{
fprintf(f, "%s\t%d\t0\t0\t0\t0\n", bed->name, bedTotalBlockSize(bed));
optionallyPrintBedPlus(bedF, bed, fieldCount, 0);
}
}
}
verbose(1, "\n");
}
void doEnrichmentsFromBigWig(struct sqlConnection *conn,
struct cdwFile *ef, struct cdwValidFile *vf,
struct cdwAssembly *assembly, struct target *targetList)
/* Figure out enrichments from a bigBed file. */
{
/* Get path to bigBed, open it, and read all chromosomes. */
char *bigWigPath = cdwPathForFileId(conn, ef->id);
struct bbiFile *bbi = bigWigFileOpen(bigWigPath);
struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
struct bigWigValsOnChrom *valsOnChrom = bigWigValsOnChromNew();
/* This takes a while, so let's figure out what parts take the time. */
long totalBigQueryTime = 0;
long totalOverlapTime = 0;
/* Do a pretty complex loop that just aims to set target->overlapBases and ->uniqOverlapBases
* for all targets. This is complicated by just wanting to keep one chromosome worth of
* bigWig data in memory. Also just for performance we do a lookup of target range tree to
* get chromosome specific one to use, which avoids a hash lookup in the inner loop. */
for (chrom = chromList; chrom != NULL; chrom = chrom->next)
{
long startBigQueryTime = clock1000();
boolean gotData = bigWigValsOnChromFetchData(valsOnChrom, chrom->name, bbi);
long endBigQueryTime = clock1000();
totalBigQueryTime += endBigQueryTime - startBigQueryTime;
if (gotData)
{
double *valBuf = valsOnChrom->valBuf;
Bits *covBuf = valsOnChrom->covBuf;
/* Loop through all targets adding overlaps from ivList */
long startOverlapTime = clock1000();
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct genomeRangeTree *grt = target->grt;
struct rbTree *targetTree = genomeRangeTreeFindRangeTree(grt, chrom->name);
if (targetTree != NULL)
{
struct range *range, *rangeList = rangeTreeList(targetTree);
for (range = rangeList; range != NULL; range = range->next)
{
int s = range->start, e = range->end, i;
for (i=s; i<=e; ++i)
{
if (bitReadOne(covBuf, i))
{
double x = valBuf[i];
target->uniqOverlapBases += 1;
target->overlapBases += x;
}
}
}
}
}
long endOverlapTime = clock1000();
totalOverlapTime += endOverlapTime - startOverlapTime;
}
}
verbose(1, "totalBig %0.3f, totalOverlap %0.3f\n", 0.001*totalBigQueryTime, 0.001*totalOverlapTime);
/* Now loop through targets and save enrichment info to database */
struct target *target;
for (target = targetList; target != NULL; target = target->next)
{
if (target->skip)
continue;
struct cdwQaEnrich *enrich = enrichFromOverlaps(ef, vf, assembly, target,
target->overlapBases, target->uniqOverlapBases);
cdwQaEnrichSaveToDb(conn, enrich, "cdwQaEnrich", 128);
cdwQaEnrichFree(&enrich);
}
bigWigValsOnChromFree(&valsOnChrom);
bbiChromInfoFreeList(&chromList);
bigWigFileClose(&bbi);
freez(&bigWigPath);
}
