bool DsrcCompressorMT::Process(const InputParameters &args_)
{
IFastqStreamReader* fileReader = NULL;
DsrcFileWriter* fileWriter = NULL;
// make reusable
//
FastqDataPool* fastqPool = NULL;
FastqDataQueue* fastqQueue = NULL;
DsrcDataPool* dsrcPool = NULL;
DsrcDataQueue* dsrcQueue = NULL;
ErrorHandler* errorHandler = NULL;
//
//
FastqReader* dataReader = NULL;
DsrcWriter* dataWriter = NULL;
FastqDatasetType datasetType;
CompressionSettings compSettings = GetCompressionSettings(args_);
try
{
if (args_.useFastqStdIo)
fileReader = new FastqStdIoReader();
else
fileReader = new FastqFileReader(args_.inputFilename);
fileWriter = new DsrcFileWriter();
fileWriter->StartCompress(args_.outputFilename);
const uint32 partNum = (args_.fastqBufferSizeMB < 128) ? args_.threadNum * 4 : args_.threadNum * 2;
fastqPool = new FastqDataPool(partNum, args_.fastqBufferSizeMB << 20); // maxPart, bufferPartSize
fastqQueue = new FastqDataQueue(partNum, 1); // maxPart, threadCount
dsrcPool = new DsrcDataPool(partNum, args_.fastqBufferSizeMB << 20);
dsrcQueue = new DsrcDataQueue(partNum, args_.threadNum);
if (args_.calculateCrc32)
errorHandler = new MultithreadedErrorHandler();
else
errorHandler = new ErrorHandler();
dataReader = new FastqReader(*fileReader, *fastqQueue, *fastqPool, *errorHandler);
dataWriter = new DsrcWriter(*fileWriter, *dsrcQueue, *dsrcPool, *errorHandler);
// analyze file
//
const bool findQOffset = args_.qualityOffset == fq::FastqDatasetType::AutoQualityOffset;
if (!findQOffset)
datasetType.qualityOffset = args_.qualityOffset;
if (!dataReader->AnalyzeFirstChunk(datasetType, findQOffset))
{
throw DsrcException("Error analyzing FASTQ dataset");
}
fileWriter->SetDatasetType(datasetType);
fileWriter->SetCompressionSettings(compSettings);
}
catch (const std::runtime_error& e_)
{
AddError(e_.what());
}
if (!IsError())
{
const uint32 threadsNum = args_.threadNum;
// launch threads
//
th::thread readerThread(th::ref(*dataReader));
std::vector<DsrcCompressor*> operators;
operators.resize(threadsNum);
#ifdef USE_BOOST_THREAD
boost::thread_group opThreadGroup; // why C++11 does not have thread_group? ://
for (uint32 i = 0; i < threadsNum; ++i)
{
operators[i] = new DsrcCompressor(*fastqQueue, *fastqPool, *dsrcQueue, *dsrcPool, *errorHandler, datasetType, compSettings);
opThreadGroup.create_thread(th::ref(*operators[i]));
}
(*dataWriter)(); // main thread works as writer
readerThread.join();
opThreadGroup.join_all();
#else
std::vector<th::thread> opThreadGroup;
for (uint32 i = 0; i < threadsNum; ++i)
{
operators[i] = new DsrcCompressor(*fastqQueue, *fastqPool, *dsrcQueue, *dsrcPool, *errorHandler, datasetType, compSettings);
opThreadGroup.push_back(th::thread(th::ref(*operators[i])));
}
(*dataWriter)();
readerThread.join();
// find difference: 'for (std::vector<th::thread>::iterator i = opThreadGroup.begin(); i != opThreadGroup.end(); ++i)'
// --> 'for (auto& t : opThreadGroup)'
for (th::thread& t : opThreadGroup)
{
t.join();
}
#endif
// check for errors
//
if (errorHandler->IsError())
AddError(errorHandler->GetError());
// free resources, cleanup
//
fastqQueue->Reset();
dsrcQueue->Reset();
for (uint32 i = 0; i < threadsNum; ++i)
{
delete operators[i];
}
fileReader->Close();
fileWriter->FinishCompress();
// set log
//
fq::StreamsInfo rawSize = fileWriter->GetFastqStreamInfo();
fq::StreamsInfo compSize = fileWriter->GetDsrcStreamInfo();
std::ostringstream ss;
ss << "Compressed streams sizes (in bytes)\n";
ss << "TAG: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::MetaStream] + compSize.sizes[fq::StreamsInfo::TagStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::TagStream] << '\n';
ss << "DNA: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::DnaStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::DnaStream] << '\n';
ss << "QUA: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::QualityStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::QualityStream] << '\n';
AddLog(ss.str());
}
TFree(dataWriter);
TFree(dataReader);
TFree(errorHandler);
// make reusable
//
TFree(dsrcQueue);
TFree(dsrcPool);
TFree(fastqQueue);
TFree(fastqPool);
//
//
TFree(fileWriter);
TFree(fileReader);
return !IsError();
}
bool DsrcCompressorST::Process(const InputParameters &args_)
{
ASSERT(!IsError());
IFastqStreamReader* reader = NULL;
DsrcFileWriter* writer = NULL;
// make reusable
//
DsrcDataChunk* dsrcChunk = NULL;
FastqDataChunk* fastqChunk = NULL;
//
//
FastqDatasetType datasetType;
CompressionSettings settings = GetCompressionSettings(args_);
try
{
if (args_.useFastqStdIo)
reader = new FastqStdIoReader();
else
reader = new FastqFileReader(args_.inputFilename);
// join into constructor for RAII style
writer = new DsrcFileWriter();
writer->StartCompress(args_.outputFilename);
dsrcChunk = new DsrcDataChunk(DsrcDataChunk::DefaultBufferSize);
fastqChunk = new FastqDataChunk(args_.fastqBufferSizeMB << 20);
// analyze the header
//
const bool findQOffset = args_.qualityOffset == fq::FastqDatasetType::AutoQualityOffset;
if (!findQOffset)
{
datasetType.qualityOffset = args_.qualityOffset;
}
FastqParser parser;
if (!reader->ReadNextChunk(fastqChunk) || parser.Analyze(*fastqChunk, datasetType, findQOffset) == 0)
{
throw DsrcException("Error analyzing FASTQ dataset");
}
writer->SetDatasetType(datasetType);
writer->SetCompressionSettings(settings);
}
catch (const std::runtime_error& e_)
{
AddError(e_.what());
}
if (!IsError())
{
BitMemoryWriter bitMemory(dsrcChunk->data);
BlockCompressor superblock(datasetType, settings);
do
{
superblock.Store(bitMemory, dsrcChunk->rawStreamsInfo, dsrcChunk->compStreamsInfo, *fastqChunk);
bitMemory.Flush();
dsrcChunk->size = bitMemory.Position();
writer->WriteNextChunk(dsrcChunk);
if (args_.calculateCrc32)
{
BitMemoryReader reader(dsrcChunk->data.Pointer(), dsrcChunk->data.Size());
std::fill(fastqChunk->data.Pointer(), fastqChunk->data.Pointer() + fastqChunk->data.Size(), 0xCC);
if (!superblock.VerifyChecksum(reader, *fastqChunk))
{
AddError("CRC32 checksums mismatch.");
break;
}
}
fastqChunk->Reset();
dsrcChunk->Reset();
bitMemory.Reset();
}
while (reader->ReadNextChunk(fastqChunk));
reader->Close();
writer->FinishCompress();
// set log
//
fq::StreamsInfo rawSize = writer->GetFastqStreamInfo();
fq::StreamsInfo compSize = writer->GetDsrcStreamInfo();
std::ostringstream ss;
ss << "Compressed streams sizes (in bytes)\n";
ss << "TAG: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::MetaStream] + compSize.sizes[fq::StreamsInfo::TagStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::TagStream] << '\n';
ss << "DNA: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::DnaStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::DnaStream] << '\n';
ss << "QUA: " << std::setw(16) << compSize.sizes[fq::StreamsInfo::QualityStream]
<< " / " << std::setw(16) << rawSize.sizes[fq::StreamsInfo::QualityStream] << '\n';
AddLog(ss.str());
}
// make reusable
//
TFree(fastqChunk);
TFree(dsrcChunk);
//
//
TFree(writer);
TFree(reader);
return !IsError();
}
void BinModule::Fastq2Bin(const std::vector<std::string> &inFastqFiles_, const std::string &outBinFile_,
uint32 threadNum_, bool compressedInput_, bool verboseMode_)
{
// TODO: try/catch to free resources
//
IFastqStreamReader* fastqFile = NULL;
if (compressedInput_)
fastqFile = new MultiFastqFileReaderGz(inFastqFiles_);
else
fastqFile = new MultiFastqFileReader(inFastqFiles_);
BinFileWriter binFile;
binFile.StartCompress(outBinFile_, config);
const uint32 minimizersCount = config.minimizer.TotalMinimizersCount();
if (threadNum_ > 1)
{
FastqChunkPool* fastqPool = NULL;
FastqChunkQueue* fastqQueue = NULL;
BinaryPartsPool* binPool = NULL;
BinaryPartsQueue* binQueue = NULL;
FastqChunkReader* fastqReader = NULL;
BinChunkWriter* binWriter = NULL;
const uint32 partNum = threadNum_ * 4;
fastqPool = new FastqChunkPool(partNum, config.fastqBlockSize);
fastqQueue = new FastqChunkQueue(partNum, 1);
binPool = new BinaryPartsPool(partNum, minimizersCount);
binQueue = new BinaryPartsQueue(partNum, threadNum_);
fastqReader = new FastqChunkReader(fastqFile, fastqQueue, fastqPool);
binWriter = new BinChunkWriter(&binFile, binQueue, binPool);
// launch stuff
//
mt::thread readerThread(mt::ref(*fastqReader));
std::vector<IOperator*> operators;
operators.resize(threadNum_);
#ifdef USE_BOOST_THREAD
boost::thread_group opThreadGroup;
for (uint32 i = 0; i < threadNum_; ++i)
{
operators[i] = new BinEncoder(config.minimizer, config.catParams,
fastqQueue, fastqPool,
binQueue, binPool);
opThreadGroup.create_thread(mt::ref(*operators[i]));
}
(*binWriter)();
readerThread.join();
opThreadGroup.join_all();
#else
std::vector<mt::thread> opThreadGroup;
for (uint32 i = 0; i < threadNum_; ++i)
{
operators[i] = new BinEncoder(config.minimizer, config.catParams,
fastqQueue, fastqPool, binQueue, binPool);
opThreadGroup.push_back(mt::thread(mt::ref(*operators[i])));
}
(*binWriter)();
readerThread.join();
for (mt::thread& t : opThreadGroup)
{
t.join();
}
#endif
for (uint32 i = 0; i < threadNum_; ++i)
{
delete operators[i];
}
TFREE(binWriter);
TFREE(fastqReader);
TFREE(binQueue);
TFREE(binPool);
TFREE(fastqQueue);
TFREE(fastqPool);
}
else
{
DnaParser parser;
DnaCategorizer categorizer(config.minimizer, config.catParams);
DnaPacker packer(config.minimizer);
DataChunk fastqChunk(config.fastqBlockSize);
std::vector<DnaRecord> records;
records.resize(1 << 10);
DnaBinBlock dnaBins(minimizersCount);
BinaryBinBlock binBins;
DataChunk dnaBuffer;
while (fastqFile->ReadNextChunk(&fastqChunk))
{
uint64 recordsCount = 0;
parser.ParseFrom(fastqChunk, dnaBuffer, records, recordsCount);
ASSERT(recordsCount > 0);
categorizer.Categorize(records, recordsCount, dnaBins);
packer.PackToBins(dnaBins, binBins);
binFile.WriteNextBlock(&binBins);
}
}
binFile.FinishCompress();
if (verboseMode_)
{
std::vector<uint64> recordCounts;
binFile.GetBinStats(recordCounts);
std::cout << "Signatures count: " << recordCounts.size() << std::endl;
std::cout << "Records distribution in bins by signature:\n";
for (uint32 i = 0; i < recordCounts.size(); ++i)
{
if (recordCounts[i] > 0)
std::cout << i << " : " << recordCounts[i] << '\n';
}
std::cout << std::endl;
}
delete fastqFile;
}
