static struct bbiSummary *bedWriteReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList,
int fieldCount, struct lineFile *lf, bits32 initialReduction, bits32 initialReductionCount,
int zoomIncrement, int blockSize, int itemsPerSlot, boolean doCompress,
struct lm *lm, FILE *f, bits64 *retDataStart, bits64 *retIndexStart,
struct bbiSummaryElement *totalSum)
/* Write out data reduced by factor of initialReduction. Also calculate and keep in memory
* next reduction level. This is more work than some ways, but it keeps us from having to
* keep the first reduction entirely in memory. */
{
struct bbiSummary *twiceReducedList = NULL;
bits32 doubleReductionSize = initialReduction * zoomIncrement;
struct bbiChromUsage *usage = usageList;
struct bbiBoundsArray *boundsArray, *boundsPt, *boundsEnd;
boundsPt = AllocArray(boundsArray, initialReductionCount);
boundsEnd = boundsPt + initialReductionCount;
*retDataStart = ftell(f);
writeOne(f, initialReductionCount);
/* This gets a little complicated I'm afraid. The strategy is to:
* 1) Build up a range tree that represents coverage depth on that chromosome
* This also has the nice side effect of getting rid of overlaps.
* 2) Stream through the range tree, outputting the initial summary level and
* further reducing.
*/
boolean firstTime = TRUE;
struct bbiSumOutStream *stream = bbiSumOutStreamOpen(itemsPerSlot, f, doCompress);
for (usage = usageList; usage != NULL; usage = usage->next)
{
struct bbiSummary oneSummary, *sum = NULL;
struct rbTree *rangeTree = rangeTreeForBedChrom(lf, usage->name);
struct range *range, *rangeList = rangeTreeList(rangeTree);
for (range = rangeList; range != NULL; range = range->next)
{
/* Grab values we want from range. */
double val = ptToInt(range->val);
int start = range->start;
int end = range->end;
bits32 size = end - start;
/* Add to total summary. */
if (firstTime)
{
totalSum->validCount = size;
totalSum->minVal = totalSum->maxVal = val;
totalSum->sumData = val*size;
totalSum->sumSquares = val*val*size;
firstTime = FALSE;
}
else
{
totalSum->validCount += size;
if (val < totalSum->minVal) totalSum->minVal = val;
if (val > totalSum->maxVal) totalSum->maxVal = val;
totalSum->sumData += val*size;
totalSum->sumSquares += val*val*size;
}
/* If start past existing block then output it. */
if (sum != NULL && sum->end <= start && sum->end < usage->size)
{
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
sum = NULL;
}
/* If don't have a summary we're working on now, make one. */
if (sum == NULL)
{
oneSummary.chromId = usage->id;
oneSummary.start = start;
oneSummary.end = start + initialReduction;
if (oneSummary.end > usage->size) oneSummary.end = usage->size;
oneSummary.minVal = oneSummary.maxVal = val;
oneSummary.sumData = oneSummary.sumSquares = 0.0;
oneSummary.validCount = 0;
sum = &oneSummary;
}
/* Deal with case where might have to split an item between multiple summaries. This
* loop handles all but the final affected summary in that case. */
while (end > sum->end)
{
/* Fold in bits that overlap with existing summary and output. */
int overlap = rangeIntersection(start, end, sum->start, sum->end);
assert(overlap > 0);
verbose(3, "Splitting size %d at %d, overlap %d\n", end - start, sum->end, overlap);
sum->validCount += overlap;
if (sum->minVal > val) sum->minVal = val;
if (sum->maxVal < val) sum->maxVal = val;
sum->sumData += val * overlap;
sum->sumSquares += val*val * overlap;
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
size -= overlap;
/* Move summary to next part. */
sum->start = start = sum->end;
sum->end = start + initialReduction;
if (sum->end > usage->size) sum->end = usage->size;
sum->minVal = sum->maxVal = val;
sum->sumData = sum->sumSquares = 0.0;
sum->validCount = 0;
}
/* Add to summary. */
sum->validCount += size;
if (sum->minVal > val) sum->minVal = val;
if (sum->maxVal < val) sum->maxVal = val;
sum->sumData += val * size;
sum->sumSquares += val*val * size;
}
if (sum != NULL)
{
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
}
rangeTreeFree(&rangeTree);
}
bbiSumOutStreamClose(&stream);
/* Write out 1st zoom index. */
int indexOffset = *retIndexStart = ftell(f);
assert(boundsPt == boundsEnd);
cirTreeFileBulkIndexToOpenFile(boundsArray, sizeof(boundsArray[0]), initialReductionCount,
blockSize, itemsPerSlot, NULL, bbiBoundsArrayFetchKey, bbiBoundsArrayFetchOffset,
indexOffset, f);
freez(&boundsArray);
slReverse(&twiceReducedList);
return twiceReducedList;
}
struct bbiSummary *bedGraphWriteReducedOnceReturnReducedTwice(struct bbiChromUsage *usageList,
int fieldCount, struct lineFile *lf, bits32 initialReduction, bits32 initialReductionCount,
int zoomIncrement, int blockSize, int itemsPerSlot, boolean doCompress,
struct lm *lm, FILE *f, bits64 *retDataStart, bits64 *retIndexStart,
struct bbiSummaryElement *totalSum)
/* Write out data reduced by factor of initialReduction. Also calculate and keep in memory
* next reduction level. This is more work than some ways, but it keeps us from having to
* keep the first reduction entirely in memory. */
{
struct bbiSummary *twiceReducedList = NULL;
bits32 doubleReductionSize = initialReduction * zoomIncrement;
struct bbiChromUsage *usage = usageList;
struct bbiSummary oneSummary, *sum = NULL;
struct bbiBoundsArray *boundsArray, *boundsPt, *boundsEnd;
boundsPt = AllocArray(boundsArray, initialReductionCount);
boundsEnd = boundsPt + initialReductionCount;
*retDataStart = ftell(f);
writeOne(f, initialReductionCount);
boolean firstRow = TRUE;
struct bbiSumOutStream *stream = bbiSumOutStreamOpen(itemsPerSlot, f, doCompress);
/* remove initial browser and track lines */
lineFileRemoveInitialCustomTrackLines(lf);
for (;;)
{
/* Get next line of input if any. */
char *row[5];
int rowSize = lineFileChopNext(lf, row, ArraySize(row));
/* Output last section and break if at end of file. */
if (rowSize == 0 && sum != NULL)
{
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
break;
}
/* Parse out row. */
char *chrom = row[0];
bits32 start = sqlUnsigned(row[1]);
bits32 end = sqlUnsigned(row[2]);
float val = sqlFloat(row[3]);
/* Update total summary stuff. */
bits32 size = end-start;
if (firstRow)
{
totalSum->validCount = size;
totalSum->minVal = totalSum->maxVal = val;
totalSum->sumData = val*size;
totalSum->sumSquares = val*val*size;
firstRow = FALSE;
}
else
{
totalSum->validCount += size;
if (val < totalSum->minVal) totalSum->minVal = val;
if (val > totalSum->maxVal) totalSum->maxVal = val;
totalSum->sumData += val*size;
totalSum->sumSquares += val*val*size;
}
/* If new chromosome output existing block. */
if (differentString(chrom, usage->name))
{
usage = usage->next;
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
sum = NULL;
}
/* If start past existing block then output it. */
else if (sum != NULL && sum->end <= start)
{
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
sum = NULL;
}
/* If don't have a summary we're working on now, make one. */
if (sum == NULL)
{
oneSummary.chromId = usage->id;
oneSummary.start = start;
oneSummary.end = start + initialReduction;
if (oneSummary.end > usage->size) oneSummary.end = usage->size;
oneSummary.minVal = oneSummary.maxVal = val;
oneSummary.sumData = oneSummary.sumSquares = 0.0;
oneSummary.validCount = 0;
sum = &oneSummary;
}
/* Deal with case where might have to split an item between multiple summaries. This
* loop handles all but the final affected summary in that case. */
while (end > sum->end)
{
verbose(3, "Splitting start %d, end %d, sum->start %d, sum->end %d\n", start, end, sum->start, sum->end);
/* Fold in bits that overlap with existing summary and output. */
bits32 overlap = rangeIntersection(start, end, sum->start, sum->end);
sum->validCount += overlap;
if (sum->minVal > val) sum->minVal = val;
if (sum->maxVal < val) sum->maxVal = val;
sum->sumData += val * overlap;
sum->sumSquares += val*val * overlap;
bbiOutputOneSummaryFurtherReduce(sum, &twiceReducedList, doubleReductionSize,
&boundsPt, boundsEnd, lm, stream);
size -= overlap;
/* Move summary to next part. */
sum->start = start = sum->end;
sum->end = start + initialReduction;
if (sum->end > usage->size) sum->end = usage->size;
sum->minVal = sum->maxVal = val;
sum->sumData = sum->sumSquares = 0.0;
sum->validCount = 0;
}
/* Add to summary. */
sum->validCount += size;
if (sum->minVal > val) sum->minVal = val;
if (sum->maxVal < val) sum->maxVal = val;
sum->sumData += val * size;
sum->sumSquares += val*val * size;
}
bbiSumOutStreamClose(&stream);
/* Write out 1st zoom index. */
int indexOffset = *retIndexStart = ftell(f);
assert(boundsPt == boundsEnd);
cirTreeFileBulkIndexToOpenFile(boundsArray, sizeof(boundsArray[0]), initialReductionCount,
blockSize, itemsPerSlot, NULL, bbiBoundsArrayFetchKey, bbiBoundsArrayFetchOffset,
indexOffset, f);
freez(&boundsArray);
slReverse(&twiceReducedList);
return twiceReducedList;
}
