std::string runPartialBatch(mpi::communicator world, boost::shared_ptr< MatcherInterface > &matcher, ReadSet &_contigs, std::string _contigFile, ReadSet & changedContigs,
ReadSet & finalContigs, int batchIdx, int maxContigsPerBatch, SequenceLengthType minKmerSize,
double minimumCoverage, SequenceLengthType maxKmerSize,
SequenceLengthType maxExtend, SequenceLengthType kmerStep) {
LOG_DEBUG(1, "Starting runPartialBatch(" << batchIdx << " of " << _contigs.getSize() << "): " << MemoryUtils::getMemoryUsage());
ReadSet contigs; // new global contigs file a subset of original
std::string extendLog;
for(int i = batchIdx; i < (int) _contigs.getSize() && i < batchIdx + maxContigsPerBatch; i++)
contigs.append(_contigs.getRead(i));
setGlobalReadSetConstants(world, contigs);
if (contigs.getGlobalSize() == 0)
return extendLog;
std::string contigFile = DistributedOfstreamMap::writeGlobalReadSet(world, contigs, UniqueName::generateUniqueGlobalName(".tmp-batch" + UniqueName::getOurUniqueHandle() + "-", batchIdx), ".fasta", FormatOutput::Fasta());
MatcherInterface::MatchReadResults contigReadSet = matcher->match(contigs, contigFile);
assert(contigs.getSize() == contigReadSet.size());
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, " batch " << contigs.getSize() << ". Matches made");
int numThreads = omp_get_max_threads();
std::string extendLogs[numThreads];
if (!Cap3Options::getOptions().getCap3Path().empty()) {
Cap3 cap3Instances[numThreads];
#pragma omp parallel for
for(int i = 0; i < numThreads; i++) {
extendLogs[i] = cap3Instances[i].extendContigs(contigs, contigReadSet, changedContigs, finalContigs, minimumCoverage, i, numThreads);
}
} else if (!NewblerOptions::getOptions().getNewblerPath().empty()) {
Newbler newblerInstances[numThreads];
#pragma omp parallel for
for(int i = 0; i < numThreads; i++) {
extendLogs[i] = newblerInstances[i].extendContigs(contigs, contigReadSet, changedContigs, finalContigs, minimumCoverage, i, numThreads);
}
} else {
extendLog = extendContigsWithContigExtender(contigs, contigReadSet,
changedContigs, finalContigs,
minKmerSize, minimumCoverage, maxKmerSize, maxExtend, kmerStep);
}
for(int i = 0; i < numThreads; i++)
extendLog += extendLogs[i];
unlink(contigFile.c_str());
return extendLog;
}
std::string extendContigsWithCap3(const ReadSet & contigs,
ReadSet::ReadSetVector &contigReadSet, ReadSet & changedContigs,
ReadSet & finalContigs, ReadSet::ReadSetSizeType minimumCoverage) {
std::stringstream extendLog;
int poolsWithoutMinimumCoverage = 0;
// initialize per-thread Cap3 instances
Cap3 cap3[omp_get_max_threads()];
#pragma omp parallel for
for (long i = 0; i < (long) contigs.getSize(); i++) {
const Read &oldRead = contigs.getRead(i);
Read newRead = oldRead;
SequenceLengthType oldLen = oldRead.getLength(), newLen = 0;
ReadSet::ReadSetSizeType poolSize = contigReadSet[i].getSize();
double extTime = MPI_Wtime();
if (poolSize > minimumCoverage) {
LOG_VERBOSE_OPTIONAL(2, true, "Extending " << oldRead.getName() << " with " << poolSize << " pool of reads");
newRead = cap3[omp_get_thread_num()].extendContig(oldRead, contigReadSet[i]);
newLen = newRead.getLength();
} else {
poolsWithoutMinimumCoverage++;
}
extTime = MPI_Wtime() - extTime;
long deltaLen = (long)newLen - (long)oldLen;
if (deltaLen > 0) {
extendLog << std::endl << "Cap3 Extended " << oldRead.getName() << " "
<< deltaLen << " bases to " << newRead.getLength() << ": "
<< newRead.getName() << " with " << poolSize
<< " reads in the pool, in " << extTime << " sec";
//#pragma omp critical
changedContigs.append(newRead);
} else {
extendLog << std::endl << "Did not extend " << oldRead.getName() << " with " << poolSize << " reads in the pool, in " << extTime << " sec";
//#pragma omp critical
finalContigs.append(oldRead);
}
}
LOG_VERBOSE_OPTIONAL(2, true, "Extended " << contigs.getSize() - poolsWithoutMinimumCoverage << " contigs out of " << contigs.getSize());
return extendLog.str();
}
void finishLongContigs(long maxContigLength, ReadSet &changedContigs, ReadSet &finalContigs) {
ReadSet keepContigs;
for(long i = 0; i < (long) changedContigs.getSize(); i++) {
const Read &read = changedContigs.getRead(i);
if ((long) read.getLength() >= maxContigLength) {
LOG_VERBOSE_OPTIONAL(1, true, read.getName() << " (" << read.getLength() << ") has exceeded maxContiglength, terminating extension");
finalContigs.append(read);
} else
keepContigs.append(read);
}
changedContigs.swap(keepContigs);
}
std::string extendContigsWithContigExtender(ReadSet & contigs,
ReadSet::ReadSetVector &contigReadSet, ReadSet & changedContigs,
ReadSet & finalContigs, SequenceLengthType minKmerSize,
double minimumCoverage, SequenceLengthType maxKmerSize,
SequenceLengthType maxExtend, SequenceLengthType kmerStep) {
std::stringstream extendLog;
//#pragma omp parallel for
for (ReadSet::ReadSetSizeType i = 0; i < contigs.getSize(); i++) {
const Read &oldRead = contigs.getRead(i);
Read newRead;
SequenceLengthType oldLen = oldRead.getLength(), newLen = 0;
ReadSet::ReadSetSizeType poolSize = contigReadSet[i].getSize();
SequenceLengthType myKmerSize = minKmerSize;
if (poolSize > minimumCoverage) {
LOG_VERBOSE_OPTIONAL(2, true, "kmer-Extending " << oldRead.getName() << " with " << poolSize << " pool of reads");
ReadSet myContig;
myContig.append(oldRead);
ReadSet newContig;
while (newLen <= oldLen && myKmerSize <= maxKmerSize) {
newContig = ContigExtender<KS>::extendContigs(myContig,
contigReadSet[i], maxExtend, myKmerSize, myKmerSize);
newLen = newContig.getRead(0).getLength();
myKmerSize += kmerStep;
}
newRead = newContig.getRead(0);
} else {
newRead = oldRead;
}
long deltaLen = (long) newLen - (long) oldLen;
if (deltaLen > 0) {
extendLog << std::endl << "Kmer Extended " << oldRead.getName() << " "
<< deltaLen << " bases to " << newRead.getLength() << ": "
<< newRead.getName() << " with " << poolSize
<< " reads in the pool K " << (myKmerSize - kmerStep);
//#pragma omp critical
changedContigs.append(newRead);
} else {
extendLog << std::endl << "Did not extend " << oldRead.getName() << " with " << poolSize << " reads in the pool";
//#pragma omp critical
finalContigs.append(oldRead);
}
}
return extendLog.str();
}
int main(int argc, char *argv[]) {
ForkDaemon::initialize();
ScopedMPIComm< DistributedNucleatingAssemblerOptions > world(argc, argv);
Cleanup::prepare();
try {
double timing1, timing2;
timing1 = MPI_Wtime();
OptionsBaseInterface::FileListType &inputFiles =
Options::getOptions().getInputFiles();
std::string contigFile =
ContigExtenderBaseOptions::getOptions().getContigFile();
std::string finalContigFile;
double minimumCoverage =
ContigExtenderBaseOptions::getOptions().getMinimumCoverage();
long maxIterations =
DistributedNucleatingAssemblerOptions::getOptions().getMaxIterations();
ReadSet reads;
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Reading Input Files" );
reads.appendAllFiles(inputFiles, world.rank(), world.size());
reads.identifyPairs();
setGlobalReadSetConstants(world, reads);
timing2 = MPI_Wtime();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "loaded " << reads.getGlobalSize() << " Reads, (local:" << reads.getSize() << " pair:" << reads.getPairSize() << ") in " << (timing2-timing1) << " seconds" );
LOG_DEBUG_GATHER(1, MemoryUtils::getMemoryUsage());
if (FilterKnownOdditiesOptions::getOptions().getSkipArtifactFilter() == 0) {
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Preparing artifact filter: ");
FilterKnownOddities filter;
LOG_VERBOSE_OPTIONAL(2, world.rank() == 0, "Applying sequence artifact filter to Input Files");
unsigned long filtered = filter.applyFilter(reads);
LOG_VERBOSE_GATHER(2, "local filter affected (trimmed/removed) " << filtered << " Reads ");
LOG_DEBUG_GATHER(1, MemoryUtils::getMemoryUsage());
unsigned long allFiltered;
mpi::reduce(world, filtered, allFiltered, std::plus<unsigned long>(), 0);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "distributed filter (trimmed/removed) " << allFiltered << " Reads.");
}
boost::shared_ptr< MatcherInterface > matcher;
if (KmerBaseOptions::getOptions().getKmerSize() == 0) {
matcher.reset( new Vmatch(world, UniqueName::generateHashName(inputFiles), reads) );
} else {
matcher.reset( new KmerMatch(world, reads) );
}
SequenceLengthType minKmerSize, maxKmerSize, kmerStep, maxExtend;
ContigExtender<KS>::getMinMaxKmerSize(reads, minKmerSize, maxKmerSize,
kmerStep);
maxKmerSize = boost::mpi::all_reduce(world, maxKmerSize, mpi::minimum<
SequenceLengthType>());
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Kmer size ranges: " << minKmerSize << "\t" << maxKmerSize << "\t" << kmerStep);
maxExtend = maxKmerSize;
timing1 = timing2;
timing2 = MPI_Wtime();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Prepared Matcher indexes in " << (timing2-timing1) << " seconds");
ReadSet finalContigs;
ReadSet contigs;
contigs.appendFastaFile(contigFile, world.rank(), world.size());
int maxContigsPerBatch = DistributedNucleatingAssemblerOptions::getOptions().getMaxContigsPerBatch();
short iteration = 0;
while (++iteration <= maxIterations) {
LOG_DEBUG_GATHER(1, "Iteration " << iteration << " " << MemoryUtils::getMemoryUsage());
int batchIdx = 0;
matcher->resetTimes("Start Iteration", MPI_Wtime());
setGlobalReadSetConstants(world, contigs);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Iteration: " << iteration << ". Contig File: " << contigFile << ". contains " << contigs.getGlobalSize() << " Reads");
if (contigs.getGlobalSize() == 0) {
LOG_VERBOSE_OPTIONAL(1, true, "There are no contigs to extend in " << contigFile);
break;
}
std::string extendLog;
ReadSet changedContigs;
int lastBatch = contigs.getSize();
MPI_Allreduce(MPI_IN_PLACE, &lastBatch, 1, MPI_INT, MPI_MAX, world);
LOG_DEBUG_OPTIONAL(1, world.rank() == 0, "Iteration: " << iteration << " Last batch is " << lastBatch);
while (batchIdx < lastBatch) {
extendLog += runPartialBatch(world, matcher, contigs, contigFile, changedContigs, finalContigs, batchIdx, maxContigsPerBatch, minKmerSize, minimumCoverage, maxKmerSize, maxExtend, kmerStep);
batchIdx += maxContigsPerBatch;
}
matcher->recordTime("extendContigs", MPI_Wtime());
LOG_DEBUG_GATHER(1, (extendLog));
finishLongContigs(DistributedNucleatingAssemblerOptions::getOptions().getMaxContigLength(), changedContigs, finalContigs);
LOG_DEBUG_GATHER(1, "Changed contigs: " << changedContigs.getSize() << " finalContigs: " << finalContigs.getSize());
setGlobalReadSetConstants(world, changedContigs);
setGlobalReadSetConstants(world, finalContigs);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Changed contigs: " << changedContigs.getGlobalSize() << " finalContigs: " << finalContigs.getGlobalSize());
std::string oldFinalContigFile = finalContigFile;
std::string oldContigFile = contigFile;
{
// write out the state of the contig files (so far) so we do not loose them
DistributedOfstreamMap om(world,
Options::getOptions().getOutputFile(), "");
om.setBuildInMemory();
if (finalContigs.getGlobalSize() > 0) {
std::string fileKey = "final-" + boost::lexical_cast<
std::string>(iteration);
finalContigs.writeAll(om.getOfstream(fileKey),
FormatOutput::Fasta());
finalContigFile = om.getRealFilePath(fileKey);
}
if (changedContigs.getGlobalSize() > 0) {
std::string filekey = "-inputcontigs-" + boost::lexical_cast<
std::string>(iteration) + ".fasta";
changedContigs.writeAll(om.getOfstream(filekey),
FormatOutput::Fasta());
contigFile = om.getRealFilePath(filekey);
}
contigs = changedContigs;
}
if (world.rank() == 0) {
// preserve the final contigs in case of crash
unlink(Options::getOptions().getOutputFile().c_str());
link(finalContigFile.c_str(), Options::getOptions().getOutputFile().c_str());
}
matcher->recordTime("writeFinalTime", MPI_Wtime());
if (!Log::isDebug(1) && world.rank() == 0) {
// remove most recent contig files (if not debugging)
if (!oldFinalContigFile.empty()) {
LOG_VERBOSE_OPTIONAL(1, true, "Removing " << oldFinalContigFile);
unlink(oldFinalContigFile.c_str());
}
if (ContigExtenderBaseOptions::getOptions().getContigFile().compare(
oldContigFile) != 0) {
LOG_VERBOSE_OPTIONAL(1, true, "Removing " << oldContigFile);
unlink(oldContigFile.c_str());
}
}
if (changedContigs.getGlobalSize() == 0) {
LOG_VERBOSE_OPTIONAL(1, world.rank() == 1, "No more contigs to extend " << changedContigs.getSize());
break;
}
matcher->recordTime("finishIteration", MPI_Wtime());
LOG_DEBUG_GATHER(1, matcher->getTimes("") + ". " + MemoryUtils::getMemoryUsage());
}
matcher.reset(); // release the matcher interface
if (world.rank() == 0 && !Log::isDebug(1)) {
if (ContigExtenderBaseOptions::getOptions().getContigFile().compare(
contigFile) != 0) {
LOG_DEBUG_OPTIONAL(1, true, "Removing " << contigFile);
unlink(contigFile.c_str());
}
}
// write final contigs (and any unfinished contigs still remaining)
finalContigs.append(contigs);
std::string tmpFinalFile = DistributedOfstreamMap::writeGlobalReadSet(world, finalContigs, Options::getOptions().getOutputFile(), ".tmp", FormatOutput::Fasta());
if (world.rank() == 0 && !finalContigFile.empty()) {
LOG_DEBUG_OPTIONAL(1, true, "Removing " << finalContigFile);
unlink(finalContigFile.c_str());
}
finalContigFile = tmpFinalFile;
if (world.rank() == 0) {
unlink(Options::getOptions().getOutputFile().c_str());
rename(finalContigFile.c_str(), Options::getOptions().getOutputFile().c_str());
}
finalContigFile = Options::getOptions().getOutputFile();
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Final contigs are in: " << finalContigFile);
LOG_VERBOSE_OPTIONAL(1, world.rank() == 0, "Finished");
ForkDaemon::finalize();
} catch (std::exception &e) {
LOG_ERROR(1, "DistributedNucleatingAssembler threw an exception! Aborting..." << e.what());
world.abort(1);
} catch (...) {
LOG_ERROR(1, "DistributedNucleatingAssembler threw an error!" );
world.abort(1);
}
return 0;
}
int main(int argc, char *argv[]) {
if (!Fastq2FastaOptions::parseOpts(argc, argv)) exit(1);
Cleanup::prepare();
OptionsBaseInterface::FileListType &inputs = Options::getOptions().getInputFiles();
long splitSizeBase = Fastq2FastaOptions::getOptions().getSplitSizeMegaBase() * 1000000;
ReadSet reads;
LOG_VERBOSE(1, "Reading Input Files" );
reads.appendAllFiles(inputs);
LOG_VERBOSE(1, "loaded " << reads.getSize() << " Reads, " << reads.getBaseCount()
<< " Bases ");
reads.identifyPairs();
long currentBase = 0;
OfstreamMap ofmap;
string outputFilename = Options::getOptions().getOutputFile();
bool hasOfMap = false;
ostream *out = &cout;
int partitionNum = 1;
if (!outputFilename.empty()) {
ofmap = OfstreamMap(outputFilename);
hasOfMap = true;
} else {
splitSizeBase = 0; // do not support splitting when no output is specified
}
bool splitPairs = Fastq2FastaOptions::getOptions().getSplitPairs() != 0;
string filekey;
for(ReadSet::ReadSetSizeType pairIdx = 0 ; pairIdx < reads.getPairSize(); pairIdx++) {
ReadSet::Pair pair = reads.getPair(pairIdx);
ReadSet::ReadSetSizeType lesserIdx = std::min(pair.read1, pair.read2);
if (hasOfMap) {
filekey = reads.getReadFileNamePrefix(lesserIdx);
} else {
filekey.clear();
}
if (splitSizeBase > 0) {
SequenceLengthType len = reads.getRead(lesserIdx).getLength();
currentBase += len;
if (currentBase > splitSizeBase) {
// new output handle
partitionNum++;
currentBase = len;
}
filekey += "-" + boost::lexical_cast<string>( partitionNum );
}
if (reads.isValidRead(pair.read1) && reads.isValidRead(pair.read2)) {
const Read read = reads.getRead(pair.read1);
if (hasOfMap) {
if (splitPairs) {
filekey += "-1";
}
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(pair.read1).write(*out);
if (splitPairs) {
filekey[filekey.length()-1] = '2';
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(pair.read2).write(*out);
} else {
if (hasOfMap) {
out = &( ofmap.getOfstream(filekey) );
}
reads.getRead(lesserIdx).write(*out);
}
}
}