void ExternalRunner :: run()
{
mProcess = new QProcess();
mProcess->setProcessChannelMode(QProcess::MergedChannels);
connect(mProcess, SIGNAL(finished(int)), mProcess, SLOT(deleteLater()));
connect(mProcess, SIGNAL(finished(int)), this, SLOT(quit()));
connect(mProcess, SIGNAL(readyRead()), this, SLOT(processRead()));
QString appLine = QString("%1 %2").arg(mExternal).arg(mScriptFile);
Log::info("Starting: " + appLine);
mProcess->start(appLine);
exec();
Log::info("End of the thread.");
}
//
// Main
//
int preprocessMain(int argc, char** argv)
{
Timer* pTimer = new Timer("sga preprocess");
parsePreprocessOptions(argc, argv);
std::cerr << "Parameters:\n";
std::cerr << "QualTrim: " << opt::qualityTrim << "\n";
if(opt::qualityFilter >= 0)
std::cerr << "QualFilter: at most " << opt::qualityFilter << " low quality bases\n";
else
std::cerr << "QualFilter: no filtering\n";
std::cerr << "HardClip: " << opt::hardClip << "\n";
std::cerr << "Min length: " << opt::minLength << "\n";
std::cerr << "Sample freq: " << opt::sampleFreq << "\n";
std::cerr << "PE Mode: " << opt::peMode << "\n";
std::cerr << "Quality scaling: " << opt::qualityScale << "\n";
std::cerr << "MinGC: " << opt::minGC << "\n";
std::cerr << "MaxGC: " << opt::maxGC << "\n";
std::cerr << "Outfile: " << (opt::outFile.empty() ? "stdout" : opt::outFile) << "\n";
std::cerr << "Orphan file: " << (opt::orphanFile.empty() ? "none" : opt::orphanFile) << "\n";
if(opt::bDiscardAmbiguous)
std::cerr << "Discarding sequences with ambiguous bases\n";
if(opt::bDustFilter)
std::cerr << "Dust threshold: " << opt::dustThreshold << "\n";
if(!opt::suffix.empty())
std::cerr << "Suffix: " << opt::suffix << "\n";
if(opt::adapterF.length() && opt::adapterR.length())
{
std::cerr << "Adapter sequence fwd: " << opt::adapterF << "\n";
std::cerr << "Adapter sequence rev: " << opt::adapterR << "\n";
}
// Seed the RNG
srand(time(NULL));
std::ostream* pWriter;
if(opt::outFile.empty())
{
pWriter = &std::cout;
}
else
{
std::ostream* pFile = createWriter(opt::outFile);
pWriter = pFile;
}
// Create a filehandle to write orphaned reads to, if necessary
std::ostream* pOrphanWriter = NULL;
if(!opt::orphanFile.empty())
pOrphanWriter = createWriter(opt::orphanFile);
if(opt::peMode == 0)
{
// Treat files as SE data
while(optind < argc)
{
std::string filename = argv[optind++];
std::cerr << "Processing " << filename << "\n\n";
SeqReader reader(filename, SRF_NO_VALIDATION);
SeqRecord record;
while(reader.get(record))
{
bool passed = processRead(record);
if(passed && samplePass())
{
if(!opt::suffix.empty())
record.id.append(opt::suffix);
record.write(*pWriter);
++s_numReadsKept;
s_numBasesKept += record.seq.length();
}
}
}
}
else
{
assert(opt::peMode == 1 || opt::peMode == 2);
int numFiles = argc - optind;
if(opt::peMode == 1 && numFiles % 2 == 1)
{
std::cerr << "Error: An even number of files must be given for pe-mode 1\n";
exit(EXIT_FAILURE);
}
while(optind < argc)
{
SeqReader* pReader1;
SeqReader* pReader2;
if(opt::peMode == 1)
{
// Read from separate files
std::string filename1 = argv[optind++];
std::string filename2 = argv[optind++];
pReader1 = new SeqReader(filename1, SRF_NO_VALIDATION);
pReader2 = new SeqReader(filename2, SRF_NO_VALIDATION);
std::cerr << "Processing pe files " << filename1 << ", " << filename2 << "\n";
}
else
{
// Read from a single file
std::string filename = argv[optind++];
pReader1 = new SeqReader(filename, SRF_NO_VALIDATION);
pReader2 = pReader1;
std::cerr << "Processing interleaved pe file " << filename << "\n";
}
SeqRecord record1;
SeqRecord record2;
while(pReader1->get(record1) && pReader2->get(record2))
{
// If the names of the records are the same, append a /1 and /2 to them
if(record1.id == record2.id)
{
if(!opt::suffix.empty())
{
record1.id.append(opt::suffix);
record2.id.append(opt::suffix);
}
record1.id.append("/1");
record2.id.append("/2");
}
// Ensure the read names are sensible
std::string expectedID2 = getPairID(record1.id);
std::string expectedID1 = getPairID(record2.id);
if(expectedID1 != record1.id || expectedID2 != record2.id)
{
std::cerr << "Warning: Pair IDs do not match (expected format /1,/2 or /A,/B)\n";
std::cerr << "Read1 ID: " << record1.id << "\n";
std::cerr << "Read2 ID: " << record2.id << "\n";
s_numInvalidPE += 2;
}
bool passed1 = processRead(record1);
bool passed2 = processRead(record2);
if(!samplePass())
continue;
if(passed1 && passed2)
{
record1.write(*pWriter);
record2.write(*pWriter);
s_numReadsKept += 2;
s_numBasesKept += record1.seq.length();
s_numBasesKept += record2.seq.length();
}
else if(passed1 && pOrphanWriter != NULL)
{
record1.write(*pOrphanWriter);
}
else if(passed2 && pOrphanWriter != NULL)
{
record2.write(*pOrphanWriter);
}
}
if(pReader2 != pReader1)
{
// only delete reader2 if it is a distinct pointer
delete pReader2;
pReader2 = NULL;
}
delete pReader1;
pReader1 = NULL;
}
}
if(pWriter != &std::cout)
delete pWriter;
if(pOrphanWriter != NULL)
delete pOrphanWriter;
std::cerr << "\nPreprocess stats:\n";
std::cerr << "Reads parsed:\t" << s_numReadsRead << "\n";
std::cerr << "Reads kept:\t" << s_numReadsKept << " (" << (double)s_numReadsKept / (double)s_numReadsRead << ")\n";
std::cerr << "Reads failed primer screen:\t" << s_numReadsPrimer << " (" << (double)s_numReadsPrimer / (double)s_numReadsRead << ")\n";
std::cerr << "Bases parsed:\t" << s_numBasesRead << "\n";
std::cerr << "Bases kept:\t" << s_numBasesKept << " (" << (double)s_numBasesKept / (double)s_numBasesRead << ")\n";
std::cerr << "Number of incorrectly paired reads that were discarded: " << s_numInvalidPE << "\n";
if(opt::bDustFilter)
std::cerr << "Number of reads failed dust filter: " << s_numFailedDust << "\n";
delete pTimer;
return 0;
}
