void CDaemon::handleClientRead()
{
QTcpSocket * socket = qobject_cast<QTcpSocket *>(sender());
while(socket->bytesAvailable() > 8)
{
QDataStream stream(socket);
quint64 size;
stream >> size;
if(socket->bytesAvailable() >= size)
{
QByteArray buffer(socket->read(size));
QDataStream bStream(buffer);
quint8 opcode;
bStream >> opcode;
switch(opcode)
{
case OPCODE_ADD:
handleAdd(bStream); break;
case OPCODE_REMOVE:
handleRemove(bStream); break;
case OPCODE_START:
handleStart(bStream); break;
case OPCODE_STOP:
handleAbort(bStream); break;
case OPCODE_QUEUE:
handleQueue(bStream); break;
default:
qWarning() << "Unhandled packet:" << quint32(opcode); break;
}
}
}
CommandEngine::CommandEngine(Core *parent) :
mCore(parent)
{
core()->print("CommandEngine initialized.", "CE");
queueTick = new QTimer(this);
connect(queueTick, SIGNAL(timeout()), this, SLOT(handleQueue()));
queueTick->start(150);
}
int bamfiltermc(libmaus2::util::ArgInfo const & arginfo)
{
bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(arginfo));
::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
::libmaus2::bambam::BamHeader const & header = dec.getHeader();
::libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
std::string const tmpfilenamebase = arginfo.getUnparsedValue("tmpfile",arginfo.getDefaultTmpFileName());
uint64_t const numthreads = arginfo.getValueUnsignedNumeric<uint64_t>("numthreads",getDefaultNumThreads());
/*
* start index/md5 callbacks
*/
std::string const tmpfileindex = tmpfilenamebase + "_index";
::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
std::string md5filename;
std::string indexfilename;
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo) != std::string() )
md5filename = libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo);
else
std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;
if ( md5filename.size() )
{
::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
Pmd5cb = UNIQUE_PTR_MOVE(Tmd5cb);
cbs.push_back(Pmd5cb.get());
}
}
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
{
if ( libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo) != std::string() )
indexfilename = libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo);
else
std::cerr << "[V] no filename for index given, not creating index" << std::endl;
if ( indexfilename.size() )
{
libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
Pindex = UNIQUE_PTR_MOVE(Tindex);
cbs.push_back(Pindex.get());
}
}
std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > * Pcbs = 0;
if ( cbs.size() )
Pcbs = &cbs;
/*
* end md5/index callbacks
*/
::libmaus2::bambam::BamHeader::unique_ptr_type genuphead(
libmaus2::bambam::BamHeaderUpdate::updateHeader(arginfo,header,"bamfiltermc",std::string(PACKAGE_VERSION))
);
libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pwriter(libmaus2::bambam::BamBlockWriterBaseFactory::construct(*genuphead,arginfo,Pcbs));
libmaus2::bambam::BamBlockWriterBase & wr = *Pwriter;
// freelist size
uint64_t const flsize = 16*1024;
libmaus2::util::FreeList < libmaus2::bambam::BamAlignment, BamAlignmentFreeListDefaultAllocator, BamAlignmentFreeListDefaultTypeInfo > FL(flsize);
libmaus2::util::SimpleQueue < libmaus2::bambam::BamAlignment::shared_ptr_type > Q;
libmaus2::bambam::BamAuxFilterVector auxvec;
auxvec.set('M','C');
uint64_t alcnt = 0;
while ( dec.readAlignment() )
{
if ( FL.empty() )
handleQueue(Q,FL,wr,auxvec,numthreads);
assert ( ! FL.empty() );
libmaus2::bambam::BamAlignment::shared_ptr_type P = FL.get();
P->swap(algn);
Q.push_back(P);
if ( verbose && ((++alcnt % (1024*1024)) == 0) )
std::cerr << "[V] " << alcnt << std::endl;
}
handleQueue(Q,FL,wr,auxvec,numthreads);
// reset BAM writer
Pwriter.reset();
if ( Pmd5cb )
Pmd5cb->saveDigestAsFile(md5filename);
if ( Pindex )
Pindex->flush(std::string(indexfilename));
return EXIT_SUCCESS;
}
