double twoStdsOverMean(struct bbiFile *bbi)
/* Figure out what is two standard deviations over mean for a bigWig file. This is
* an often useful threshold. */
{
struct bbiSummaryElement sum = bbiTotalSummary(bbi);
double mean = sum.sumData/sum.validCount;
double std = calcStdFromSums(sum.sumData, sum.sumSquares, sum.validCount);
return mean + 2*std;
}
double bigWigStd(struct bbiFile* bw)
/* return the mean value of a bigWig */
{
double na = NANUM;
struct bbiSummaryElement bbs = bbiTotalSummary(bw);
if (bbs.validCount == 0)
return na;
else
return calcStdFromSums(bbs.sumData, bbs.sumSquares, bbs.validCount);
}
double bigWigMean(struct bbiFile* bw)
/* return the mean value of a bigWig */
{
double na = NANUM;
struct bbiSummaryElement bbs = bbiTotalSummary(bw);
if (bbs.validCount == 0)
return na;
else
return bbs.sumData / bbs.validCount;
}
void bigWigInfo(char *fileName)
/* bigWigInfo - Print out information about bigWig file.. */
{
struct bbiFile *bwf = bigWigFileOpen(fileName);
if (optionExists("minMax"))
{
struct bbiSummaryElement sum = bbiTotalSummary(bwf);
printf("%f %f\n", sum.minVal, sum.maxVal);
return;
}
printf("version: %d\n", bwf->version);
printf("isCompressed: %s\n", (bwf->uncompressBufSize > 0 ? "yes" : "no"));
printf("isSwapped: %d\n", bwf->isSwapped);
printLabelAndLongNumber("primaryDataSize", bwf->unzoomedIndexOffset - bwf->unzoomedDataOffset);
if (bwf->levelList != NULL)
{
long long indexEnd = bwf->levelList->dataOffset;
printLabelAndLongNumber("primaryIndexSize", indexEnd - bwf->unzoomedIndexOffset);
}
printf("zoomLevels: %d\n", bwf->zoomLevels);
if (optionExists("zooms"))
{
struct bbiZoomLevel *zoom;
for (zoom = bwf->levelList; zoom != NULL; zoom = zoom->next)
printf("\t%d\t%d\n", zoom->reductionLevel, (int)(zoom->indexOffset - zoom->dataOffset));
}
struct bbiChromInfo *chrom, *chromList = bbiChromList(bwf);
printf("chromCount: %d\n", slCount(chromList));
if (optionExists("chroms"))
for (chrom=chromList; chrom != NULL; chrom = chrom->next)
printf("\t%s %d %d\n", chrom->name, chrom->id, chrom->size);
struct bbiSummaryElement sum = bbiTotalSummary(bwf);
printLabelAndLongNumber("basesCovered", sum.validCount);
printf("mean: %f\n", sum.sumData/sum.validCount);
printf("min: %f\n", sum.minVal);
printf("max: %f\n", sum.maxVal);
printf("std: %f\n", calcStdFromSums(sum.sumData, sum.sumSquares, sum.validCount));
}
struct bigBedInterval *bigBedSelectRange(struct track *track,
char *chrom, int start, int end, struct lm *lm)
/* Return list of intervals in range. */
{
struct bigBedInterval *result = NULL;
/* protect against temporary network error */
struct errCatch *errCatch = errCatchNew();
if (errCatchStart(errCatch))
{
struct bbiFile *bbi = fetchBbiForTrack(track);
int maxItems = min(BIGBEDMAXIMUMITEMS, maximumTrackItems(track)); // do not allow it to exceed BIGBEDMAXIMUMITEMS for bigBed
result = bigBedIntervalQuery(bbi, chrom, start, end, maxItems + 1, lm);
if (slCount(result) > maxItems)
{
track->limitedVis = tvDense;
track->limitedVisSet = TRUE;
result = NULL;
AllocArray(track->summary, insideWidth);
if (bigBedSummaryArrayExtended(bbi, chrom, start, end, insideWidth, track->summary))
{
char *denseCoverage = trackDbSettingClosestToHome(track->tdb, "denseCoverage");
if (denseCoverage != NULL)
{
double endVal = atof(denseCoverage);
if (endVal <= 0)
{
AllocVar(track->sumAll);
*track->sumAll = bbiTotalSummary(bbi);
}
}
}
else
freez(&track->summary);
}
bbiFileClose(&bbi);
track->bbiFile = NULL;
}
errCatchEnd(errCatch);
if (errCatch->gotError)
{
track->networkErrMsg = cloneString(errCatch->message->string);
track->drawItems = bigDrawWarning;
track->totalHeight = bigWarnTotalHeight;
result = NULL;
}
errCatchFree(&errCatch);
return result;
}
char *printBigWigViewInfo(FILE *f, char *indent, struct view *view,
struct composite *comp, struct taggedFile *tfList)
/* Print out info for a bigWig view, including subtracks. */
{
/* Look at all tracks in this view and calculate overall limits. */
double sumOfSums = 0, sumOfSumSquares = 0;
bits64 sumOfN = 0;
struct taggedFile *tf;
for (tf = tfList; tf != NULL; tf = tf->next)
{
if (sameString(tf->manifest->outputType, view->name))
{
char *relativeName = tf->manifest->fileName;
char *path = relativeName;
struct bbiFile *bbi = bigWigFileOpen(path);
struct bbiSummaryElement sum = bbiTotalSummary(bbi);
sumOfSums += sum.sumData;
sumOfSumSquares += sum.sumSquares;
sumOfN = sum.validCount;
bigWigFileClose(&bbi);
}
}
double mean = sumOfSums/sumOfN;
double std = calcStdFromSums(sumOfSums, sumOfSumSquares, sumOfN);
double clipMax = mean + 6*std;
/* Output view stanza. */
char type[64];
safef(type, sizeof(type), "bigWig %g %g", 0.0, clipMax);
fprintf(f, "%stype %s\n", indent, type);
fprintf(f, "%sviewLimits 0:%g\n", indent, clipMax);
fprintf(f, "%sminLimit 0\n", indent);
fprintf(f, "%smaxLimit %g\n", indent, clipMax);
fprintf(f, "%sautoScale off\n", indent);
fprintf(f, "%smaxHeightPixels 100:32:16\n", indent);
fprintf(f, "%swindowingFunction mean+whiskers\n", indent);
return cloneString(type);
}
