boolean bigBedSummaryArrayExtended(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
int summarySize, struct bbiSummaryElement *summary)
/* Get extended summary information for summarySize evenly spaced elements into
* the summary array. */
{
return bbiSummaryArrayExtended(bbi, chrom, start, end, bigBedCoverageIntervals,
summarySize, summary);
}
boolean bigWigSummaryArrayExtended(struct bbiFile *bwf, char *chrom, bits32 start, bits32 end,
int summarySize, struct bbiSummaryElement *summary)
/* Get extended summary information for summarySize evenely spaced elements into
* the summary array. */
{
boolean ret = bbiSummaryArrayExtended(bwf, chrom, start, end, bigWigIntervalQuery,
summarySize, summary);
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;
}
boolean bbiSummaryArray(struct bbiFile *bbi, char *chrom, bits32 start, bits32 end,
BbiFetchIntervals fetchIntervals,
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 bbiSummaryElement *elements;
AllocArray(elements, summarySize);
boolean ret = bbiSummaryArrayExtended(bbi, chrom, start, end,
fetchIntervals, summarySize, elements);
if (ret)
{
int i;
double covFactor = (double)summarySize/(end - start);
for (i=0; i<summarySize; ++i)
{
struct bbiSummaryElement *el = &elements[i];
if (el->validCount > 0)
{
double val;
switch (summaryType)
{
case bbiSumMean:
val = el->sumData/el->validCount;
break;
case bbiSumMax:
val = el->maxVal;
break;
case bbiSumMin:
val = el->minVal;
break;
case bbiSumCoverage:
val = covFactor*el->validCount;
break;
case bbiSumStandardDeviation:
val = calcStdFromSums(el->sumData, el->sumSquares, el->validCount);
break;
default:
internalErr();
val = 0.0;
break;
}
summaryValues[i] = val;
}
}
}
freeMem(elements);
return ret;
}
void doSummaryStatsBigWig(struct sqlConnection *conn)
/* Put up page showing summary stats for bigWig track. */
{
struct trackDb *track = curTrack;
char *table = curTable;
char *shortLabel = (track == NULL ? table : track->shortLabel);
char *fileName = bigWigFileName(table, conn);
long startTime = clock1000();
htmlOpen("%s (%s) Big Wig Summary Statistics", shortLabel, table);
if (anySubtrackMerge(database, curTable))
hPrintf("<P><EM><B>Note:</B> subtrack merge is currently ignored on this "
"page (not implemented yet). Statistics shown here are only for "
"the primary table %s (%s).</EM>", shortLabel, table);
struct bbiFile *bwf = bigWigFileOpen(fileName);
struct region *region, *regionList = getRegions();
double sumData = 0, sumSquares = 0, minVal = 0, maxVal = 0;
bits64 validCount = 0;
if (!anyFilter() && !anyIntersection())
{
for (region = regionList; region != NULL; region = region->next)
{
struct bbiSummaryElement sum;
if (bbiSummaryArrayExtended(bwf, region->chrom, region->start, region->end,
bigWigIntervalQuery, 1, &sum))
{
if (validCount == 0)
{
minVal = sum.minVal;
maxVal = sum.maxVal;
}
else
{
if (sum.minVal < minVal)
minVal = sum.minVal;
if (sum.maxVal > maxVal)
maxVal = sum.maxVal;
}
sumData += sum.sumData;
sumSquares += sum.sumSquares;
validCount += sum.validCount;
}
}
}
else
{
double ll, ul;
enum wigCompare cmp;
getWigFilter(database, curTable, &cmp, &ll, &ul);
for (region = regionList; region != NULL; region = region->next)
{
struct lm *lm = lmInit(0);
struct bbiInterval *iv, *ivList;
ivList = intersectedFilteredBbiIntervalsOnRegion(conn, bwf, region, cmp, ll, ul, lm);
for (iv = ivList; iv != NULL; iv = iv->next)
{
double val = iv->val;
double size = iv->end - iv->start;
if (validCount == 0)
minVal = maxVal = val;
else
{
if (val < minVal)
minVal = val;
if (val > maxVal)
maxVal = val;
}
sumData += size*val;
sumSquares += size*val*val;
validCount += size;
}
lmCleanup(&lm);
}
}
hTableStart();
floatStatRow("mean", sumData/validCount);
floatStatRow("min", minVal);
floatStatRow("max", maxVal);
floatStatRow("standard deviation", calcStdFromSums(sumData, sumSquares, validCount));
numberStatRow("bases with data", validCount);
long long regionSize = basesInRegion(regionList,0);
long long gapTotal = gapsInRegion(conn, regionList,0);
numberStatRow("bases with sequence", regionSize - gapTotal);
numberStatRow("bases in region", regionSize);
wigFilterStatRow(conn);
stringStatRow("intersection", cartUsualString(cart, hgtaIntersectTable, "off"));
long wigFetchTime = clock1000() - startTime;
floatStatRow("load and calc time", 0.001*wigFetchTime);
hTableEnd();
bbiFileClose(&bwf);
htmlClose();
}
