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RangeSplitter.cpp
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RangeSplitter.cpp
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/*++
Module Name:
RangeSplitter.cpp
Abstract:
Code to split a range into pieces for multiple cores to process. It's designed
to handle cores that proceed at varying rates.
Authors:
Bill Bolosky, 2011
Environment:
User mode service.
Revision History:
Pulled out of cSNAP.cpp to make it useful for various versions of the aligner.
Generalized from FileSplitter to ranges, e.g. for scanning the genome /ravip/5/2012/
--*/
#include "stdafx.h"
#include "RangeSplitter.h"
#include "SAM.h"
#include "FASTQ.h"
using std::max;
using std::min;
RangeSplitter::RangeSplitter(_int64 rangeEnd_, int numThreads_, unsigned divisionSize_, _int64 rangeBegin_, unsigned minMillis_, unsigned minRangeSize_)
{
numThreads = numThreads_;
rangeEnd = rangeEnd_;
rangeBegin = rangeBegin_;
position = rangeBegin_;
startTime = 0; // We'll initialize it when getNextRange() is first called
divisionSize = divisionSize_;
minMillis = minMillis_;
minRangeSize = minRangeSize_;
}
bool RangeSplitter::getNextRange(_int64 *rangeStart, _int64 *rangeLength)
{
// If there are multiple threads, start each of them off with (rangeEnd / divionSize / numThreads),
// and then keep giving everyone 1 / (divisionSize * numThreads) of the remaining data or the amount
// of units processed per thread in minMillis ms, whichever is bigger.
// If there's just one thread, we give it the whole range at the beginning.
if (startTime == 0) {
// There's a possible "race" here if multiple threads start at the same time, but that's
// actually OK; we just want a rough idea of when we started the processing.
startTime = timeInMillis();
}
_int64 amountLeft = rangeEnd - position;
if (amountLeft <= 0) {
return false;
}
_int64 amountToTake;
if (numThreads == 1) {
amountToTake = rangeEnd;
} else if (amountLeft >= (rangeEnd - rangeBegin) / divisionSize) {
amountToTake = (rangeEnd - rangeBegin) / divisionSize / numThreads;
if (amountToTake == 0) {
amountToTake = amountLeft;
} else {
amountToTake = min(amountLeft, max(amountToTake, (_int64) minRangeSize));
}
} else {
// Figure out units processed in minMillis ms per thread (keeping in mind we ran numThreads in total).
_int64 unitsInMinms = (position - rangeBegin) * minMillis / max((_int64) (timeInMillis() - startTime) * numThreads, (_int64) 1);
amountToTake = max(amountLeft / divisionSize / numThreads, unitsInMinms);
amountToTake = max(amountToTake, (_int64) minRangeSize); // Avoid getting really tiny amounts at the end.
}
_ASSERT(amountToTake > 0);
_int64 oldPosition = position; // for debugging
_int64 startOffset = InterlockedAdd64AndReturnNewValue(&position, amountToTake) - amountToTake;
_ASSERT(position >= rangeBegin);
if (startOffset >= rangeEnd) {
// No work left to allocate.
return false;
}
// Don't run past EOF if there was a race above (threads looking at amountLeft at the same time).
amountToTake = min(amountToTake, rangeEnd - startOffset);
_ASSERT(amountToTake > 0);
*rangeStart = startOffset;
*rangeLength = amountToTake;
_ASSERT(startOffset >= rangeBegin && startOffset + amountToTake <= rangeEnd);
return true;
}
RangeSplittingReadSupplierGenerator::RangeSplittingReadSupplierGenerator(
const char *i_fileName,
bool i_isSAM,
unsigned i_numThreads,
const ReaderContext& i_context)
: isSAM(i_isSAM), context(i_context), numThreads(i_numThreads)
{
fileName = new char[strlen(i_fileName) + 1];
strcpy(fileName, i_fileName);
//
// Figure out the header size based on file type. We set up the range splitter to skip the header. This both makes the work allocation more even,
// and also assures that in the case where the header is bigger than what would otherwise be the first work unit that the second guy in doesn't see
// header.
//
_int64 headerSize;
if (isSAM) {
SAMReader *reader = SAMReader::create(DataSupplier::Default, fileName, ReadSupplierQueue::BufferCount(numThreads), context, 0, 0);
if (!reader) {
WriteErrorMessage("Unable to create reader for SAM file '%s'\n", fileName);
soft_exit(1);
}
headerSize = reader->getContext()->headerBytes;
delete reader;
reader = NULL;
} else {
// FASTQ has no header.
headerSize = 0;
}
splitter = new RangeSplitter(QueryFileSize(fileName), numThreads, 5, headerSize, 200, 10 * MAX_READ_LENGTH);
}
ReadSupplier *
RangeSplittingReadSupplierGenerator::generateNewReadSupplier()
{
_int64 rangeStart, rangeLength;
if (!splitter->getNextRange(&rangeStart, &rangeLength)) {
return NULL;
}
ReadReader *underlyingReader;
// todo: implement layered factory model
if (isSAM) {
underlyingReader = SAMReader::create(DataSupplier::Default, fileName, 2, context, rangeStart, rangeLength);
} else {
underlyingReader = FASTQReader::create(DataSupplier::Default, fileName, 2, rangeStart, rangeLength, context);
}
return new RangeSplittingReadSupplier(splitter,underlyingReader);
}
RangeSplittingReadSupplier::~RangeSplittingReadSupplier()
{
}
Read *
RangeSplittingReadSupplier::getNextRead()
{
if (underlyingReader->getNextRead(&read)) {
return &read;
}
_int64 rangeStart, rangeLength;
if (!splitter->getNextRange(&rangeStart, &rangeLength)) {
return NULL;
}
underlyingReader->reinit(rangeStart,rangeLength);
if (!underlyingReader->getNextRead(&read)) {
return NULL;
}
return &read;
}
RangeSplittingPairedReadSupplier::~RangeSplittingPairedReadSupplier()
{
}
bool
RangeSplittingPairedReadSupplier::getNextReadPair(Read **read1, Read **read2)
{
*read1 = &internalRead1;
*read2 = &internalRead2;
if (underlyingReader->getNextReadPair(&internalRead1,&internalRead2)) {
return true;
}
//
// We need to clear out the reads, because they may contain references to the buffers in the readers.
// These buffer reference counts get reset to 0 at reinit time, which causes problems when they're
// still live in read.
//
_int64 rangeStart, rangeLength;
if (!splitter->getNextRange(&rangeStart, &rangeLength)) {
return false;
}
underlyingReader->reinit(rangeStart,rangeLength);
return underlyingReader->getNextReadPair(&internalRead1, &internalRead2);
}
RangeSplittingPairedReadSupplierGenerator::RangeSplittingPairedReadSupplierGenerator(
const char *i_fileName1, const char *i_fileName2, FileType i_fileType, unsigned i_numThreads,
bool i_quicklyDropUnpairedReads, const ReaderContext& i_context) :
fileType(i_fileType), numThreads(i_numThreads), context(i_context), quicklyDropUnpairedReads(i_quicklyDropUnpairedReads)
{
_ASSERT(strcmp(i_fileName1, "-") && (NULL == i_fileName2 || strcmp(i_fileName2, "-"))); // Can't use range splitter on stdin, because you can't seek or query size
fileName1 = new char[strlen(i_fileName1) + 1];
strcpy(fileName1, i_fileName1);
if (FASTQFile == fileType) {
fileName2 = new char[strlen(i_fileName2) + 1];
strcpy(fileName2, i_fileName2);
} else {
fileName2 = NULL;
}
splitter = new RangeSplitter(QueryFileSize(fileName1),numThreads);
}
RangeSplittingPairedReadSupplierGenerator::~RangeSplittingPairedReadSupplierGenerator()
{
delete [] fileName1;
delete [] fileName2;
delete splitter;
}
PairedReadSupplier *
RangeSplittingPairedReadSupplierGenerator::generateNewPairedReadSupplier()
{
_int64 rangeStart, rangeLength;
if (!splitter->getNextRange(&rangeStart, &rangeLength)) {
return NULL;
}
PairedReadReader *underlyingReader;
switch (fileType) {
case SAMFile:
underlyingReader = SAMReader::createPairedReader(DataSupplier::Default, fileName1, 2, rangeStart, rangeLength, quicklyDropUnpairedReads, context);
break;
case FASTQFile:
underlyingReader = PairedFASTQReader::create(DataSupplier::Default, fileName1, fileName2, 2, rangeStart, rangeLength, context);
break;
case InterleavedFASTQFile:
underlyingReader = PairedInterleavedFASTQReader::create(DataSupplier::Default, fileName1, 2, rangeStart, rangeLength, context);
break;
default:
WriteErrorMessage("RangeSplittingPairedReadSupplierGenerator::generateNewPairedReadSupplier(): unknown file type %d\n", fileType);
soft_exit(1);
}
return new RangeSplittingPairedReadSupplier(splitter,underlyingReader);
}