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/*++
Module Name:
ToFASTQ.cpp
Abstract:
Take a set of reads in SAM or BAM format and convert them to FASTQ
Authors:
Bill Bolosky, January, 2014
Environment:
`
User mode service.
Revision History:
--*/
#include "stdafx.h"
#include "SAM.h"
#include "Bam.h"
#include "Genome.h"
#include "Compat.h"
#include "Read.h"
#include "RangeSplitter.h"
#include "BigAlloc.h"
#include "FASTQ.h"
void usage()
{
fprintf(stderr,"usage: ToFASTQ genomeIndex inputFile outputFile {outputFile2}\n");
fprintf(stderr," Specifying two output files means that the input is paired. If you specify only one output file, then\n");
fprintf(stderr," ToFASTQ will generate a single-ended FASTQ even for a paired input.\n");
fprintf(stderr," The genomeIndex must contain the same set of contigs used to align the input file.\n");
fprintf(stderr," To produce interleaved paired-end FASTQ, specify outputFile2 as '-i'.\n");
soft_exit(1);
}
ReadSupplierGenerator *readSupplierGenerator = NULL;
volatile _int64 nRunningThreads;
SingleWaiterObject allThreadsDone;
const char *inputFileName;
const Genome *genome;
FASTQWriter *fastqWriter[2] = {NULL, NULL};
struct ThreadContext {
unsigned whichThread;
_int64 totalReads;
ThreadContext() {
totalReads = 0;
}
};
bool inline isADigit(char x) {
return x >= '0' && x <= '9';
}
void
WorkerThreadMain(void *param)
{
ThreadContext *context = (ThreadContext *)param;
ReadSupplier *readSupplier = readSupplierGenerator->generateNewReadSupplier();
Read *read;
while (NULL != (read = readSupplier->getNextRead())) {
context->totalReads++;
fastqWriter[0]->writeRead(read);
} // for each read from the reader
if (0 == InterlockedAdd64AndReturnNewValue(&nRunningThreads, -1)) {
SignalSingleWaiterObject(&allThreadsDone);
}
}
_int64
ProcessPairedInput(PairedReadSupplierGenerator *pairedReadSupplierGenerator)
{
//
// This runs single threaded, because it's the only easy way to assure that the two output files match.
//
PairedReadSupplier *readSupplier = pairedReadSupplierGenerator->generateNewPairedReadSupplier();
Read *read[NUM_READS_PER_PAIR];
const size_t idBufferSize = 10000;
char idBuffer[idBufferSize];
_int64 totalReads = 0;
while (readSupplier->getNextReadPair(&read[0], &read[1])) {
for (int i = 0; i < NUM_READS_PER_PAIR; i++) {
//
// Create a new read with an ID that includes /1 or /2. Don't bother to fill in the stuff that the
// FASTQ writer doesn't care about anyway.
//
snprintf(idBuffer, idBufferSize-1,"%.*s/%d", read[i]->getIdLength(), read[i]->getId(), i+1);
Read local;
local.init(idBuffer, (unsigned)strlen(idBuffer),read[i]->getUnclippedData(), read[i]->getUnclippedQuality(), read[i]->getUnclippedLength(),
0,0,0,0,0,0,0,NULL,0,0);
fastqWriter[i]->writeRead(&local);
}
totalReads += 2;
}
return totalReads;
}
int main(int argc, char * argv[])
{
BigAllocUseHugePages = false;
if (4 != argc && 5 != argc) usage();
static const char *genomeSuffix = "Genome";
size_t filenameLen = strlen(argv[1]) + 1 + strlen(genomeSuffix) + 1;
char *fileName = new char[strlen(argv[1]) + 1 + strlen(genomeSuffix) + 1];
snprintf(fileName,filenameLen,"%s%c%s",argv[1],PATH_SEP,genomeSuffix);
genome = Genome::loadFromFile(fileName, 0);
if (NULL == genome) {
fprintf(stderr,"Unable to load genome from file '%s'\n",fileName);
return -1;
}
delete [] fileName;
fileName = NULL;
inputFileName = argv[2];
fastqWriter[0] = FASTQWriter::Factory(argv[3]);
if (NULL == fastqWriter[0]) {
fprintf(stderr,"Unable to open FASTQ writer for output file '%s'\n", argv[3]);
soft_exit(1);
}
_int64 totalReads = 0;
unsigned nThreads;
#ifdef _DEBUG
nThreads = 1;
#else // _DEBUG
if (5 == argc) {
nThreads = 1;
} else {
nThreads = GetNumberOfProcessors();
}
#endif // _DEBUG
DataSupplier::ThreadCount = nThreads;
nRunningThreads = nThreads;
ReaderContext readerContext;
readerContext.clipping = NoClipping;
readerContext.defaultReadGroup = "";
readerContext.genome = genome;
readerContext.ignoreSecondaryAlignments = true;
readerContext.ignoreSupplementaryAlignments = true;
readerContext.preserveFASTQComments = false;
readerContext.header = NULL;
readerContext.headerLength = 0;
readerContext.headerBytes = 0;
if (5 == argc) {
if (!strcmp(argv[4], "-i")) {
fastqWriter[1] = fastqWriter[0]; // Interleaved
} else {
fastqWriter[1] = FASTQWriter::Factory(argv[4]);
if (NULL == fastqWriter[1]) {
fprintf(stderr,"Unable to open FASTQ writer for output file '%s'\n", argv[4]);
soft_exit(1);
}
}
PairedReadSupplierGenerator *pairedReadSupplierGenerator;
if (NULL != strrchr(inputFileName, '.') && !_stricmp(strrchr(inputFileName, '.'), ".bam")) {
pairedReadSupplierGenerator = BAMReader::createPairedReadSupplierGenerator(inputFileName, nThreads, true, readerContext);
} else {
pairedReadSupplierGenerator = SAMReader::createPairedReadSupplierGenerator(inputFileName, nThreads, true, readerContext);
}
totalReads = ProcessPairedInput(pairedReadSupplierGenerator);
if (fastqWriter[1] != fastqWriter[0]) {
delete fastqWriter[1];
} else {
fastqWriter[1] = NULL;
}
} else {
if (NULL != strrchr(inputFileName, '.') && !_stricmp(strrchr(inputFileName, '.'), ".bam")) {
readSupplierGenerator = BAMReader::createReadSupplierGenerator(inputFileName, nThreads, readerContext);
} else {
readSupplierGenerator = SAMReader::createReadSupplierGenerator(inputFileName, nThreads, readerContext);
}
CreateSingleWaiterObject(&allThreadsDone);
ThreadContext *contexts = new ThreadContext[nThreads];
for (unsigned i = 0; i < nThreads; i++) {
contexts[i].whichThread = i;
StartNewThread(WorkerThreadMain, &contexts[i]);
}
WaitForSingleWaiterObject(&allThreadsDone);
for (unsigned i = 0; i < nThreads; i++) {
totalReads += contexts[i].totalReads;
}
}
printf("%lld reads\n", totalReads);
delete fastqWriter[0];
return 0;
}
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