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peprocessor.cpp
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#include "peprocessor.h"
#include "fastqreader.h"
#include <iostream>
#include <unistd.h>
#include <functional>
#include <thread>
#include <memory.h>
#include "util.h"
#include "adaptertrimmer.h"
#include "basecorrector.h"
#include "jsonreporter.h"
#include "htmlreporter.h"
#include "polyx.h"
PairEndProcessor::PairEndProcessor(Options* opt){
mOptions = opt;
mLeftReaderFinished = false;
mRightReaderFinished = false;
mFinishedThreads = 0;
mFilter = new Filter(opt);
mUmiProcessor = new UmiProcessor(opt);
int isizeBufLen = mOptions->insertSizeMax + 1;
mInsertSizeHist = new atomic_long[isizeBufLen];
memset(mInsertSizeHist, 0, sizeof(atomic_long)*isizeBufLen);
mLeftWriter = NULL;
mRightWriter = NULL;
mUnpairedLeftWriter = NULL;
mUnpairedRightWriter = NULL;
mMergedWriter = NULL;
mFailedWriter = NULL;
mOverlappedWriter = NULL;
mDuplicate = NULL;
if(mOptions->duplicate.enabled) {
mDuplicate = new Duplicate(mOptions);
}
mLeftPackReadCounter = 0;
mRightPackReadCounter = 0;
mPackProcessedCounter = 0;
mLeftReadPool = new ReadPool(mOptions);
mRightReadPool = new ReadPool(mOptions);
}
PairEndProcessor::~PairEndProcessor() {
delete mInsertSizeHist;
if(mDuplicate) {
delete mDuplicate;
mDuplicate = NULL;
}
if(mLeftReadPool) {
delete mLeftReadPool;
mLeftReadPool = NULL;
}
if(mRightReadPool) {
delete mRightReadPool;
mRightReadPool = NULL;
}
}
void PairEndProcessor::initOutput() {
if(!mOptions->unpaired1.empty())
mUnpairedLeftWriter = new WriterThread(mOptions, mOptions->unpaired1);
if(!mOptions->unpaired2.empty() && mOptions->unpaired2 != mOptions->unpaired1)
mUnpairedRightWriter = new WriterThread(mOptions, mOptions->unpaired2);
if(mOptions->merge.enabled) {
if(!mOptions->merge.out.empty())
mMergedWriter = new WriterThread(mOptions, mOptions->merge.out);
}
if(!mOptions->failedOut.empty())
mFailedWriter = new WriterThread(mOptions, mOptions->failedOut);
if(!mOptions->overlappedOut.empty())
mOverlappedWriter = new WriterThread(mOptions, mOptions->overlappedOut);
if(mOptions->out1.empty())
return;
mLeftWriter = new WriterThread(mOptions, mOptions->out1);
if(!mOptions->out2.empty())
mRightWriter = new WriterThread(mOptions, mOptions->out2);
}
void PairEndProcessor::closeOutput() {
if(mLeftWriter) {
delete mLeftWriter;
mLeftWriter = NULL;
}
if(mRightWriter) {
delete mRightWriter;
mRightWriter = NULL;
}
if(mMergedWriter) {
delete mMergedWriter;
mMergedWriter = NULL;
}
if(mFailedWriter) {
delete mFailedWriter;
mFailedWriter = NULL;
}
if(mOverlappedWriter) {
delete mOverlappedWriter;
mOverlappedWriter = NULL;
}
if(mUnpairedLeftWriter) {
delete mUnpairedLeftWriter;
mUnpairedLeftWriter = NULL;
}
if(mUnpairedRightWriter) {
delete mUnpairedRightWriter;
mUnpairedRightWriter = NULL;
}
}
void PairEndProcessor::initConfig(ThreadConfig* config) {
if(mOptions->out1.empty())
return;
if(mOptions->split.enabled) {
config->initWriterForSplit();
}
}
bool PairEndProcessor::process(){
if(!mOptions->split.enabled)
initOutput();
std::thread* readerLeft = NULL;
std::thread* readerRight = NULL;
std::thread* readerInterveleaved = NULL;
mLeftInputLists = new SingleProducerSingleConsumerList<ReadPack*>*[mOptions->thread];
mRightInputLists = new SingleProducerSingleConsumerList<ReadPack*>*[mOptions->thread];
ThreadConfig** configs = new ThreadConfig*[mOptions->thread];
for(int t=0; t<mOptions->thread; t++){
mLeftInputLists[t] = new SingleProducerSingleConsumerList<ReadPack*>();
mRightInputLists[t] = new SingleProducerSingleConsumerList<ReadPack*>();
configs[t] = new ThreadConfig(mOptions, t, true);
configs[t]->setInputListPair(mLeftInputLists[t], mRightInputLists[t]);
initConfig(configs[t]);
}
if(mOptions->interleavedInput)
readerInterveleaved= new std::thread(std::bind(&PairEndProcessor::interleavedReaderTask, this));
else {
readerLeft = new std::thread(std::bind(&PairEndProcessor::readerTask, this, true));
readerRight = new std::thread(std::bind(&PairEndProcessor::readerTask, this, false));
}
std::thread** threads = new thread*[mOptions->thread];
for(int t=0; t<mOptions->thread; t++){
threads[t] = new std::thread(std::bind(&PairEndProcessor::processorTask, this, configs[t]));
}
std::thread* leftWriterThread = NULL;
std::thread* rightWriterThread = NULL;
std::thread* unpairedLeftWriterThread = NULL;
std::thread* unpairedRightWriterThread = NULL;
std::thread* mergedWriterThread = NULL;
std::thread* failedWriterThread = NULL;
std::thread* overlappedWriterThread = NULL;
if(mLeftWriter)
leftWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mLeftWriter));
if(mRightWriter)
rightWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mRightWriter));
if(mUnpairedLeftWriter)
unpairedLeftWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mUnpairedLeftWriter));
if(mUnpairedRightWriter)
unpairedRightWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mUnpairedRightWriter));
if(mMergedWriter)
mergedWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mMergedWriter));
if(mFailedWriter)
failedWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mFailedWriter));
if(mOverlappedWriter)
overlappedWriterThread = new std::thread(std::bind(&PairEndProcessor::writerTask, this, mOverlappedWriter));
if(readerInterveleaved) {
readerInterveleaved->join();
} else {
readerLeft->join();
readerRight->join();
}
for(int t=0; t<mOptions->thread; t++){
threads[t]->join();
}
if(!mOptions->split.enabled) {
if(leftWriterThread)
leftWriterThread->join();
if(rightWriterThread)
rightWriterThread->join();
if(unpairedLeftWriterThread)
unpairedLeftWriterThread->join();
if(unpairedRightWriterThread)
unpairedRightWriterThread->join();
if(mergedWriterThread)
mergedWriterThread->join();
if(failedWriterThread)
failedWriterThread->join();
if(overlappedWriterThread)
overlappedWriterThread->join();
}
if(mOptions->verbose)
loginfo("start to generate reports\n");
// merge stats and filter results
vector<Stats*> preStats1;
vector<Stats*> postStats1;
vector<Stats*> preStats2;
vector<Stats*> postStats2;
vector<FilterResult*> filterResults;
for(int t=0; t<mOptions->thread; t++){
preStats1.push_back(configs[t]->getPreStats1());
postStats1.push_back(configs[t]->getPostStats1());
preStats2.push_back(configs[t]->getPreStats2());
postStats2.push_back(configs[t]->getPostStats2());
filterResults.push_back(configs[t]->getFilterResult());
}
Stats* finalPreStats1 = Stats::merge(preStats1);
Stats* finalPostStats1 = Stats::merge(postStats1);
Stats* finalPreStats2 = Stats::merge(preStats2);
Stats* finalPostStats2 = Stats::merge(postStats2);
FilterResult* finalFilterResult = FilterResult::merge(filterResults);
cerr << "Read1 before filtering:"<<endl;
finalPreStats1->print();
cerr << endl;
cerr << "Read2 before filtering:"<<endl;
finalPreStats2->print();
cerr << endl;
if(!mOptions->merge.enabled) {
cerr << "Read1 after filtering:"<<endl;
finalPostStats1->print();
cerr << endl;
cerr << "Read2 after filtering:"<<endl;
finalPostStats2->print();
} else {
cerr << "Merged and filtered:"<<endl;
finalPostStats1->print();
}
cerr << endl;
cerr << "Filtering result:"<<endl;
finalFilterResult->print();
double dupRate = 0.0;
if(mOptions->duplicate.enabled) {
dupRate = mDuplicate->getDupRate();
cerr << endl;
cerr << "Duplication rate: " << dupRate * 100.0 << "%" << endl;
}
// insert size distribution
int peakInsertSize = getPeakInsertSize();
cerr << endl;
cerr << "Insert size peak (evaluated by paired-end reads): " << peakInsertSize << endl;
if(mOptions->merge.enabled) {
cerr << endl;
cerr << "Read pairs merged: " << finalFilterResult->mMergedPairs << endl;
if(finalPostStats1->getReads() > 0) {
double postMergedPercent = 100.0 * finalFilterResult->mMergedPairs / finalPostStats1->getReads();
double preMergedPercent = 100.0 * finalFilterResult->mMergedPairs / finalPreStats1->getReads();
cerr << "% of original read pairs: " << preMergedPercent << "%" << endl;
cerr << "% in reads after filtering: " << postMergedPercent << "%" << endl;
}
cerr << endl;
}
// make JSON report
JsonReporter jr(mOptions);
jr.setDup(dupRate);
jr.setInsertHist(mInsertSizeHist, peakInsertSize);
jr.report(finalFilterResult, finalPreStats1, finalPostStats1, finalPreStats2, finalPostStats2);
// make HTML report
HtmlReporter hr(mOptions);
hr.setDup(dupRate);
hr.setInsertHist(mInsertSizeHist, peakInsertSize);
hr.report(finalFilterResult, finalPreStats1, finalPostStats1, finalPreStats2, finalPostStats2);
// clean up
for(int t=0; t<mOptions->thread; t++){
delete threads[t];
threads[t] = NULL;
delete configs[t];
configs[t] = NULL;
}
if(readerInterveleaved) {
delete readerInterveleaved;
} else {
delete readerLeft;
delete readerRight;
}
delete finalPreStats1;
delete finalPostStats1;
delete finalPreStats2;
delete finalPostStats2;
delete finalFilterResult;
delete[] threads;
delete[] configs;
if(leftWriterThread)
delete leftWriterThread;
if(rightWriterThread)
delete rightWriterThread;
if(unpairedLeftWriterThread)
delete unpairedLeftWriterThread;
if(unpairedRightWriterThread)
delete unpairedRightWriterThread;
if(mergedWriterThread)
delete mergedWriterThread;
if(failedWriterThread)
delete failedWriterThread;
if(overlappedWriterThread)
delete overlappedWriterThread;
if(!mOptions->split.enabled)
closeOutput();
return true;
}
int PairEndProcessor::getPeakInsertSize() {
int peak = 0;
long maxCount = -1;
for(int i=0; i<mOptions->insertSizeMax; i++) {
if(mInsertSizeHist[i] > maxCount) {
peak = i;
maxCount = mInsertSizeHist[i];
}
}
return peak;
}
void PairEndProcessor::recycleToPool1(int tid, Read* r) {
// failed to recycle, then delete it
if(!mLeftReadPool->input(tid, r))
delete r;
}
void PairEndProcessor::recycleToPool2(int tid, Read* r) {
// failed to recycle, then delete it
if(!mRightReadPool->input(tid, r))
delete r;
}
bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, ThreadConfig* config){
if(leftPack->count != rightPack->count) {
cerr << endl;
cerr << "WARNING: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
cerr << "Read1 pack size: " << leftPack->count << endl;
cerr << "Read2 pack size: " << rightPack->count << endl;
cerr << endl;
error_exit("input files don't contain identical amount of reads");
}
int tid = config->getThreadId();
string* outstr1 = new string();
string* outstr2 = new string();
string* unpairedOut1 = new string();
string* unpairedOut2 = new string();
string* singleOutput = new string();
string* mergedOutput = new string();
string* failedOut = new string();
string* overlappedOut = new string();
int readPassed = 0;
int mergedCount = 0;
for(int p=0;p<leftPack->count && p<rightPack->count;p++){
Read* or1 = leftPack->data[p];
Read* or2 = rightPack->data[p];
int lowQualNum1 = 0;
int nBaseNum1 = 0;
int lowQualNum2 = 0;
int nBaseNum2 = 0;
// stats the original read before trimming
config->getPreStats1()->statRead(or1);
config->getPreStats2()->statRead(or2);
// handling the duplication profiling
bool dedupOut = false;
if(mDuplicate) {
bool isDup = mDuplicate->checkPair(or1, or2);
if(mOptions->duplicate.dedup && isDup)
dedupOut = true;
}
// filter by index
if(mOptions->indexFilter.enabled && mFilter->filterByIndex(or1, or2)) {
recycleToPool1(tid, or1);
or1 = NULL;
recycleToPool2(tid, or2);
or2 = NULL;
continue;
}
// fix MGI
if(mOptions->fixMGI) {
or1->fixMGI();
or2->fixMGI();
}
// umi processing
if(mOptions->umi.enabled)
mUmiProcessor->process(or1, or2);
// trim in head and tail, and apply quality cut in sliding window
int frontTrimmed1 = 0;
int frontTrimmed2 = 0;
Read* r1 = mFilter->trimAndCut(or1, mOptions->trim.front1, mOptions->trim.tail1, frontTrimmed1);
Read* r2 = mFilter->trimAndCut(or2, mOptions->trim.front2, mOptions->trim.tail2, frontTrimmed2);
if(r1 != NULL && r2!=NULL) {
if(mOptions->polyGTrim.enabled)
PolyX::trimPolyG(r1, r2, config->getFilterResult(), mOptions->polyGTrim.minLen);
}
bool isizeEvaluated = false;
if(r1 != NULL && r2!=NULL && (mOptions->adapter.enabled || mOptions->correction.enabled)){
OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, mOptions->overlapDiffPercentLimit/100.0);
// we only use thread 0 to evaluae ISIZE
if(config->getThreadId() == 0) {
statInsertSize(r1, r2, ov, frontTrimmed1, frontTrimmed2);
isizeEvaluated = true;
}
if(mOptions->correction.enabled) {
BaseCorrector::correctByOverlapAnalysis(r1, r2, config->getFilterResult(), ov);
}
if(mOptions->adapter.enabled) {
bool trimmed = AdapterTrimmer::trimByOverlapAnalysis(r1, r2, config->getFilterResult(), ov, frontTrimmed1, frontTrimmed2);
bool trimmed1 = trimmed;
bool trimmed2 = trimmed;
if(!trimmed){
if(mOptions->adapter.hasSeqR1)
trimmed1 = AdapterTrimmer::trimBySequence(r1, config->getFilterResult(), mOptions->adapter.sequence, false);
if(mOptions->adapter.hasSeqR2)
trimmed2 = AdapterTrimmer::trimBySequence(r2, config->getFilterResult(), mOptions->adapter.sequenceR2, true);
}
if(mOptions->adapter.hasFasta) {
AdapterTrimmer::trimByMultiSequences(r1, config->getFilterResult(), mOptions->adapter.seqsInFasta, false, !trimmed1);
AdapterTrimmer::trimByMultiSequences(r2, config->getFilterResult(), mOptions->adapter.seqsInFasta, true, !trimmed2);
}
}
}
if(r1 != NULL && r2!=NULL && mOverlappedWriter) {
OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, 0);
if(ov.overlapped) {
Read* overlappedRead = new Read(r1->mName, new string(r1->mSeq->substr(max(0,ov.offset)), ov.overlap_len), r1->mStrand, new string(r1->mQuality->substr(max(0,ov.offset)), ov.overlap_len));
overlappedRead->appendToString(overlappedOut);
recycleToPool1(tid, overlappedRead);
}
}
if(config->getThreadId() == 0 && !isizeEvaluated && r1 != NULL && r2!=NULL) {
OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, mOptions->overlapDiffPercentLimit/100.0);
statInsertSize(r1, r2, ov, frontTrimmed1, frontTrimmed2);
isizeEvaluated = true;
}
if(r1 != NULL && r2!=NULL) {
if(mOptions->polyXTrim.enabled)
PolyX::trimPolyX(r1, r2, config->getFilterResult(), mOptions->polyXTrim.minLen);
}
if(r1 != NULL && r2!=NULL) {
if( mOptions->trim.maxLen1 > 0 && mOptions->trim.maxLen1 < r1->length())
r1->resize(mOptions->trim.maxLen1);
if( mOptions->trim.maxLen2 > 0 && mOptions->trim.maxLen2 < r2->length())
r2->resize(mOptions->trim.maxLen2);
}
Read* merged = NULL;
// merging mode
bool mergeProcessed = false;
if(mOptions->merge.enabled && r1 && r2) {
OverlapResult ov = OverlapAnalysis::analyze(r1, r2, mOptions->overlapDiffLimit, mOptions->overlapRequire, mOptions->overlapDiffPercentLimit/100.0);
if(ov.overlapped) {
merged = OverlapAnalysis::merge(r1, r2, ov);
int result = mFilter->passFilter(merged);
config->addFilterResult(result, 2);
if(result == PASS_FILTER) {
merged->appendToString(mergedOutput);
config->getPostStats1()->statRead(merged);
readPassed++;
mergedCount++;
}
recycleToPool1(tid, merged);
mergeProcessed = true;
} else if(mOptions->merge.includeUnmerged){
int result1 = mFilter->passFilter(r1);
config->addFilterResult(result1, 1);
if(result1 == PASS_FILTER && !dedupOut) {
r1->appendToString(mergedOutput);
config->getPostStats1()->statRead(r1);
}
int result2 = mFilter->passFilter(r2);
config->addFilterResult(result2, 1);
if(result2 == PASS_FILTER && !dedupOut) {
r2->appendToString(mergedOutput);
config->getPostStats1()->statRead(r2);
}
if(result1 == PASS_FILTER && result2 == PASS_FILTER )
readPassed++;
mergeProcessed = true;
}
}
if(!mergeProcessed) {
int result1 = mFilter->passFilter(r1);
int result2 = mFilter->passFilter(r2);
config->addFilterResult(max(result1, result2), 2);
if(!dedupOut) {
if( r1 != NULL && result1 == PASS_FILTER && r2 != NULL && result2 == PASS_FILTER ) {
if(mOptions->outputToSTDOUT && !mOptions->merge.enabled) {
r1->appendToString(singleOutput);
r2->appendToString(singleOutput);
} else {
r1->appendToString(outstr1);
r2->appendToString(outstr2);
}
// stats the read after filtering
if(!mOptions->merge.enabled) {
config->getPostStats1()->statRead(r1);
config->getPostStats2()->statRead(r2);
}
readPassed++;
} else if( r1 != NULL && result1 == PASS_FILTER) {
if(mUnpairedLeftWriter) {
r1->appendToString(unpairedOut1);
if(mFailedWriter)
or2->appendToStringWithTag(failedOut, FAILED_TYPES[result2]);
} else {
if(mFailedWriter) {
or1->appendToStringWithTag(failedOut, "paired_read_is_failing");
or2->appendToStringWithTag(failedOut, FAILED_TYPES[result2]);
}
}
} else if( r2 != NULL && result2 == PASS_FILTER) {
if(mUnpairedRightWriter) {
r2->appendToString(unpairedOut2);
if(mFailedWriter)
or1->appendToStringWithTag(failedOut,FAILED_TYPES[result1]);
} else if(mUnpairedLeftWriter) {
r2->appendToString(unpairedOut1);
if(mFailedWriter)
or1->appendToStringWithTag(failedOut,FAILED_TYPES[result1]);
} else {
if(mFailedWriter) {
or1->appendToStringWithTag(failedOut, FAILED_TYPES[result1]);
or2->appendToStringWithTag(failedOut, "paired_read_is_failing");
}
}
}
}
}
// if no trimming applied, r1 should be identical to or1
if(r1 != or1 && r1 != NULL) {
recycleToPool1(tid, r1);
r1 = NULL;
}
// if no trimming applied, r1 should be identical to or1
if(r2 != or2 && r2 != NULL) {
recycleToPool2(tid, r2);
r2 = NULL;
}
if(or1) {
recycleToPool1(tid, or1);
or1 = NULL;
}
if(or2) {
recycleToPool2(tid, or2);
or2 = NULL;
}
}
if(mOptions->outputToSTDOUT) {
// STDOUT output
// if it's merging mode, write the merged reads to STDOUT
// otherwise write interleaved single output
if(mOptions->merge.enabled)
fwrite(mergedOutput->c_str(), 1, mergedOutput->length(), stdout);
else
fwrite(singleOutput->c_str(), 1, singleOutput->length(), stdout);
} else if(mOptions->split.enabled) {
// split output by each worker thread
if(!mOptions->out1.empty())
config->getWriter1()->writeString(outstr1);
if(!mOptions->out2.empty())
config->getWriter2()->writeString(outstr2);
}
if(mMergedWriter) {
// write merged data
mMergedWriter->input(tid, mergedOutput);
mergedOutput = NULL;
}
if(mFailedWriter) {
// write failed data
mFailedWriter->input(tid, failedOut);
failedOut = NULL;
}
if(mOverlappedWriter) {
// write failed data
mOverlappedWriter->input(tid, overlappedOut);
overlappedOut = NULL;
}
// normal output by left/right writer thread
if(mRightWriter && mLeftWriter) {
// write PE
mLeftWriter->input(tid, outstr1);
outstr1 = NULL;
mRightWriter->input(tid, outstr2);
outstr2 = NULL;
} else if(mLeftWriter) {
// write singleOutput
mLeftWriter->input(tid, singleOutput);
singleOutput = NULL;
}
// output unpaired reads
if(mUnpairedLeftWriter && mUnpairedRightWriter) {
// write PE
mUnpairedLeftWriter->input(tid, unpairedOut1);
unpairedOut1 = NULL;
mUnpairedRightWriter->input(tid, unpairedOut2);
unpairedOut2 = NULL;
} else if(mUnpairedLeftWriter) {
mUnpairedLeftWriter->input(tid, unpairedOut1);
unpairedOut1 = NULL;
}
if(mOptions->split.byFileLines)
config->markProcessed(readPassed);
else
config->markProcessed(leftPack->count);
if(mOptions->merge.enabled) {
config->addMergedPairs(mergedCount);
}
if(outstr1)
delete outstr1;
if(outstr2)
delete outstr2;
if(unpairedOut1)
delete unpairedOut1;
if(unpairedOut2)
delete unpairedOut2;
if(singleOutput)
delete singleOutput;
if(mergedOutput)
delete mergedOutput;
if(failedOut)
delete failedOut;
if(overlappedOut)
delete overlappedOut;
delete leftPack->data;
delete rightPack->data;
delete leftPack;
delete rightPack;
mPackProcessedCounter++;
return true;
}
void PairEndProcessor::statInsertSize(Read* r1, Read* r2, OverlapResult& ov, int frontTrimmed1, int frontTrimmed2) {
int isize = mOptions->insertSizeMax;
if(ov.overlapped) {
if(ov.offset > 0)
isize = r1->length() + r2->length() - ov.overlap_len + frontTrimmed1 + frontTrimmed2;
else
isize = ov.overlap_len + frontTrimmed1 + frontTrimmed2;
}
if(isize > mOptions->insertSizeMax)
isize = mOptions->insertSizeMax;
mInsertSizeHist[isize]++;
}
void PairEndProcessor::readerTask(bool isLeft)
{
if(mOptions->verbose) {
if(isLeft)
loginfo("start to load data of read1");
else
loginfo("start to load data of read2");
}
long lastReported = 0;
int slept = 0;
long readNum = 0;
bool splitSizeReEvaluated = false;
Read** data = new Read*[PACK_SIZE];
memset(data, 0, sizeof(Read*)*PACK_SIZE);
FastqReader* reader = NULL;
if(isLeft) {
reader = new FastqReader(mOptions->in1, true, mOptions->phred64);
reader->setReadPool(mLeftReadPool);
}
else {
reader = new FastqReader(mOptions->in2, true, mOptions->phred64);
reader->setReadPool(mRightReadPool);
}
int count=0;
bool needToBreak = false;
while(true){
Read* read = reader->read();
if(!read || needToBreak){
// the last pack
ReadPack* pack = new ReadPack;
pack->data = data;
pack->count = count;
if(isLeft) {
mLeftInputLists[mLeftPackReadCounter % mOptions->thread]->produce(pack);
mLeftPackReadCounter++;
} else {
mRightInputLists[mRightPackReadCounter % mOptions->thread]->produce(pack);
mRightPackReadCounter++;
}
data = NULL;
if(read) {
delete read;
read = NULL;
}
break;
}
data[count] = read;
count++;
// configured to process only first N reads
if(mOptions->readsToProcess >0 && count + readNum >= mOptions->readsToProcess) {
needToBreak = true;
}
if(mOptions->verbose && count + readNum >= lastReported + 1000000) {
lastReported = count + readNum;
string msg;
if(isLeft)
msg = "Read1: ";
else
msg = "Read2: ";
msg += "loaded " + to_string((lastReported/1000000)) + "M reads";
loginfo(msg);
}
// a full pack
if(count == PACK_SIZE || needToBreak){
ReadPack* pack = new ReadPack;
pack->data = data;
pack->count = count;
if(isLeft) {
mLeftInputLists[mLeftPackReadCounter % mOptions->thread]->produce(pack);
mLeftPackReadCounter++;
} else {
mRightInputLists[mRightPackReadCounter % mOptions->thread]->produce(pack);
mRightPackReadCounter++;
}
//re-initialize data for next pack
data = new Read*[PACK_SIZE];
memset(data, 0, sizeof(Read*)*PACK_SIZE);
// if the processor is far behind this reader, sleep and wait to limit memory usage
if(isLeft) {
while(mLeftPackReadCounter - mPackProcessedCounter > PACK_IN_MEM_LIMIT){
//cerr<<"sleep"<<endl;
slept++;
usleep(100);
}
} else {
while(mRightPackReadCounter - mPackProcessedCounter > PACK_IN_MEM_LIMIT){
//cerr<<"sleep"<<endl;
slept++;
usleep(100);
}
}
readNum += count;
// if the writer threads are far behind this producer, sleep and wait
// check this only when necessary
if(readNum % (PACK_SIZE * PACK_IN_MEM_LIMIT) == 0 && mLeftWriter) {
while( (mLeftWriter && mLeftWriter->bufferLength() > PACK_IN_MEM_LIMIT) || (mRightWriter && mRightWriter->bufferLength() > PACK_IN_MEM_LIMIT) ){
slept++;
usleep(1000);
}
}
// reset count to 0
count = 0;
// re-evaluate split size
// TODO: following codes are commented since it may cause threading related conflicts in some systems
/*if(mOptions->split.needEvaluation && !splitSizeReEvaluated && readNum >= mOptions->split.size) {
splitSizeReEvaluated = true;
// greater than the initial evaluation
if(readNum >= 1024*1024) {
size_t bytesRead;
size_t bytesTotal;
reader.getBytes(bytesRead, bytesTotal);
mOptions->split.size *= (double)bytesTotal / ((double)bytesRead * (double) mOptions->split.number);
if(mOptions->split.size <= 0)
mOptions->split.size = 1;
}
}*/
}
}
for(int t=0; t<mOptions->thread; t++) {
if(isLeft)
mLeftInputLists[t]->setProducerFinished();
else
mRightInputLists[t]->setProducerFinished();
}
if(mOptions->verbose) {
if(isLeft) {
mLeftReaderFinished = true;
loginfo("Read1: loading completed with " + to_string(mLeftPackReadCounter) + " packs");
}
else {
mRightReaderFinished = true;
loginfo("Read2: loading completed with " + to_string(mRightPackReadCounter) + " packs");
}
}
// if the last data initialized is not used, free it
if(data != NULL)
delete[] data;
if(reader != NULL)
delete reader;
}
void PairEndProcessor::interleavedReaderTask()
{
if(mOptions->verbose)
loginfo("start to load data");
long lastReported = 0;
int slept = 0;
long readNum = 0;
bool splitSizeReEvaluated = false;
Read** dataLeft = new Read*[PACK_SIZE];
Read** dataRight = new Read*[PACK_SIZE];
memset(dataLeft, 0, sizeof(Read*)*PACK_SIZE);
memset(dataRight, 0, sizeof(Read*)*PACK_SIZE);
FastqReaderPair reader(mOptions->in1, mOptions->in2, true, mOptions->phred64,true);
int count=0;
bool needToBreak = false;
while(true){
ReadPair* pair = reader.read();
// TODO: put needToBreak here is just a WAR for resolve some unidentified dead lock issue
if(!pair || needToBreak){
// the last pack
ReadPack* packLeft = new ReadPack;
ReadPack* packRight = new ReadPack;
packLeft->data = dataLeft;
packRight->data = dataRight;
packLeft->count = count;
packRight->count = count;
mLeftInputLists[mLeftPackReadCounter % mOptions->thread]->produce(packLeft);
mLeftPackReadCounter++;
mRightInputLists[mRightPackReadCounter % mOptions->thread]->produce(packRight);
mRightPackReadCounter++;
dataLeft = NULL;
dataRight = NULL;
if(pair) {
delete pair;
pair = NULL;
}
break;
}
dataLeft[count] = pair->mLeft;
dataRight[count] = pair->mRight;
count++;
// configured to process only first N reads
if(mOptions->readsToProcess >0 && count + readNum >= mOptions->readsToProcess) {
needToBreak = true;
}
if(mOptions->verbose && count + readNum >= lastReported + 1000000) {
lastReported = count + readNum;
string msg = "loaded " + to_string((lastReported/1000000)) + "M read pairs";
loginfo(msg);
}
// a full pack
if(count == PACK_SIZE || needToBreak){
ReadPack* packLeft = new ReadPack;
ReadPack* packRight = new ReadPack;
packLeft->data = dataLeft;
packRight->data = dataRight;
packLeft->count = count;
packRight->count = count;
mLeftInputLists[mLeftPackReadCounter % mOptions->thread]->produce(packLeft);
mLeftPackReadCounter++;
mRightInputLists[mRightPackReadCounter % mOptions->thread]->produce(packRight);
mRightPackReadCounter++;
//re-initialize data for next pack
dataLeft = new Read*[PACK_SIZE];
dataRight = new Read*[PACK_SIZE];
memset(dataLeft, 0, sizeof(Read*)*PACK_SIZE);
memset(dataRight, 0, sizeof(Read*)*PACK_SIZE);
// if the consumer is far behind this producer, sleep and wait to limit memory usage
while(mLeftPackReadCounter - mPackProcessedCounter > PACK_IN_MEM_LIMIT){
//cerr<<"sleep"<<endl;
slept++;
usleep(100);
}
readNum += count;
// if the writer threads are far behind this producer, sleep and wait
// check this only when necessary
if(readNum % (PACK_SIZE * PACK_IN_MEM_LIMIT) == 0 && mLeftWriter) {
while( (mLeftWriter && mLeftWriter->bufferLength() > PACK_IN_MEM_LIMIT) || (mRightWriter && mRightWriter->bufferLength() > PACK_IN_MEM_LIMIT) ){
slept++;
usleep(1000);
}
}
// reset count to 0
count = 0;
// re-evaluate split size
// TODO: following codes are commented since it may cause threading related conflicts in some systems
/*if(mOptions->split.needEvaluation && !splitSizeReEvaluated && readNum >= mOptions->split.size) {
splitSizeReEvaluated = true;
// greater than the initial evaluation
if(readNum >= 1024*1024) {
size_t bytesRead;
size_t bytesTotal;
reader.mLeft->getBytes(bytesRead, bytesTotal);
mOptions->split.size *= (double)bytesTotal / ((double)bytesRead * (double) mOptions->split.number);
if(mOptions->split.size <= 0)
mOptions->split.size = 1;
}
}*/
}
}
for(int t=0; t<mOptions->thread; t++) {
mLeftInputLists[t]->setProducerFinished();
mRightInputLists[t]->setProducerFinished();
}
if(mOptions->verbose) {
loginfo("interleaved: loading completed with " + to_string(mLeftPackReadCounter) + " packs");
}
mLeftReaderFinished = true;
mRightReaderFinished = true;
// if the last data initialized is not used, free it
if(dataLeft != NULL)
delete[] dataLeft;
if(dataRight != NULL)
delete[] dataRight;
}
void PairEndProcessor::processorTask(ThreadConfig* config)
{
SingleProducerSingleConsumerList<ReadPack*>* inputLeft = config->getLeftInput();
SingleProducerSingleConsumerList<ReadPack*>* inputRight = config->getRightInput();
while(true) {
if(config->canBeStopped()){
break;
}
while(inputLeft->canBeConsumed() && inputRight->canBeConsumed()) {
ReadPack* dataLeft = inputLeft->consume();
ReadPack* dataRight = inputRight->consume();
processPairEnd(dataLeft, dataRight, config);
}
if(inputLeft->isProducerFinished() && !inputLeft->canBeConsumed()) {
break;
} else if(inputRight->isProducerFinished() && !inputRight->canBeConsumed()) {
break;