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C++ ArgInfo::getValue方法代码示例

本文整理汇总了C++中libmaus2::util::ArgInfo::getValue方法的典型用法代码示例。如果您正苦于以下问题：C++ ArgInfo::getValue方法的具体用法？C++ ArgInfo::getValue怎么用？C++ ArgInfo::getValue使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类libmaus2::util::ArgInfo的用法示例。


在下文中一共展示了ArgInfo::getValue方法的3个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: bamfiltermc

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));

//.........这里部分代码省略.........
开发者ID:gt1，项目名称:biobambam2，代码行数:101，代码来源:bamfiltermc.cpp

示例2: bamvalidateTemplate

int bamvalidateTemplate(::libmaus2::util::ArgInfo const & arginfo)
{
	libmaus2::timing::RealTimeClock rtc; rtc.start();
	bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
	bool const basequalhist = arginfo.getValue("basequalhist",getDefaultBaseQualHist());

	libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
		libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
			arginfo,false // put rank
		)
	);
	::libmaus2::bambam::BamAlignmentDecoder * ppdec = &(decwrapper->getDecoder());
	::libmaus2::bambam::BamAlignmentDecoder & dec = *ppdec;
	::libmaus2::bambam::BamHeader const & header = dec.getHeader();
	::libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();

	// add PG line to header
	std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
		header.text,
		"bamvalidate", // ID
		"bamvalidate", // PN
		arginfo.commandline, // CL
		::libmaus2::bambam::ProgramHeaderLineSet(header.text).getLastIdInChain(), // PP
		std::string(PACKAGE_VERSION) // VN
	);
	// construct new header
	::libmaus2::bambam::BamHeader uphead(upheadtext);

	/*
	 * start index/md5 callbacks and alignment writer
	 */
	std::string md5filename;
	std::string indexfilename;

	std::vector< ::libmaus2::lz::BgzfDeflateOutputCallback * > cbs;
	::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Pmd5cb;
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pout;

	if ( passthrough )
	{
		std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
		std::string const tmpfileindex = tmpfilenamebase + "_index";
		::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);

		if ( arginfo.getValue<unsigned int>("md5",getDefaultMD5()) )
		{
			if ( arginfo.hasArg("md5filename") &&  arginfo.getUnparsedValue("md5filename","") != "" )
				md5filename = arginfo.getUnparsedValue("md5filename","");
			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());
			}
		}
		if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
		{
			if ( arginfo.hasArg("indexfilename") &&  arginfo.getUnparsedValue("indexfilename","") != "" )
				indexfilename = arginfo.getUnparsedValue("indexfilename","");
			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;


		libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Tout (
			libmaus2::bambam::BamBlockWriterBaseFactory::construct(uphead, arginfo, Pcbs)
		);
		Pout = UNIQUE_PTR_MOVE(Tout);
	}

	libmaus2::autoarray::AutoArray<char> lastvalidname(256); // max valid read name is 255 bytes
	uint64_t alsok = 0;

	::libmaus2::autoarray::AutoArray<char> qual;
	libmaus2::autoarray::AutoArray<uint64_t> H(static_cast<uint64_t>(std::numeric_limits<uint8_t>::max())+1);
	std::fill(H.begin(),H.end(),0ull);

	try
	{
		while ( dec.readAlignment() )
		{
			if ( passthrough )
				Pout->writeAlignment(algn);

			if ( basequalhist )
			{
//.........这里部分代码省略.........
开发者ID:amcpherson，项目名称:biobambam2，代码行数:101，代码来源:bamvalidate.cpp

示例3: bamheap2

int bamheap2(libmaus2::util::ArgInfo const & arginfo)
{
	bool const verbose = arginfo.getValue("verbose",getDefaultVerbose());
	std::string const reference = arginfo.getUnparsedValue("reference",std::string());
	std::string const outputprefix = arginfo.getUnparsedValue("outputprefix",std::string());

	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 const & algn = dec.getAlignment();

	double const damult = arginfo.getValue<double>("amult",1);
	double const dcmult = arginfo.getValue<double>("cmult",1);
	double const dgmult = arginfo.getValue<double>("gmult",1);
	double const dtmult = arginfo.getValue<double>("tmult",1);
	double const dpadmult = arginfo.getValue<double>("padmult",1);

	double maxmult = 0;
	maxmult = std::max(damult,maxmult);
	maxmult = std::max(dcmult,maxmult);
	maxmult = std::max(dgmult,maxmult);
	maxmult = std::max(dtmult,maxmult);
	maxmult = std::max(dpadmult,maxmult);

	uint64_t const amult = std::floor((damult / maxmult) * (1ull<<16) + 0.5);
	uint64_t const cmult = std::floor((dcmult / maxmult) * (1ull<<16) + 0.5);
	uint64_t const gmult = std::floor((dgmult / maxmult) * (1ull<<16) + 0.5);
	uint64_t const tmult = std::floor((dtmult / maxmult) * (1ull<<16) + 0.5);
	uint64_t const padmult = std::floor((dpadmult / maxmult) * (1ull<<16) + 0.5);

	libmaus2::fastx::FastAIndex::unique_ptr_type Pindex;
	libmaus2::aio::InputStreamInstance::unique_ptr_type PCIS;
	if ( reference.size() )
	{
		libmaus2::fastx::FastAIndex::unique_ptr_type Tindex(
			libmaus2::fastx::FastAIndex::load(reference+".fai")
		);
		Pindex = UNIQUE_PTR_MOVE(Tindex);

		libmaus2::aio::InputStreamInstance::unique_ptr_type TCIS(new libmaus2::aio::InputStreamInstance(reference));
		PCIS = UNIQUE_PTR_MOVE(TCIS);
	}

	libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigop;
	libmaus2::autoarray::AutoArray<char> bases;

	int64_t prevrefid = -1;
	std::string refidname = "*";

	std::map< uint64_t, HeapEntry > M;
	uint64_t alcnt = 0;
	std::vector< std::pair<char,uint8_t> > pendinginserts;
	int64_t loadedRefId = -1;
	int64_t streamRefId = -1;
	libmaus2::autoarray::AutoArray<char> refseqbases;
	ConsensusAccuracy * consacc = 0;
	std::map<uint64_t,ConsensusAccuracy> Mconsacc;
	typedef libmaus2::util::shared_ptr<std::ostringstream>::type stream_ptr_type;
	stream_ptr_type Pstream;
	ConsensusAux Caux;

	Caux.M['a'] = Caux.M['A'] = amult;
	Caux.M['c'] = Caux.M['C'] = cmult;
	Caux.M['g'] = Caux.M['G'] = gmult;
	Caux.M['t'] = Caux.M['T'] = tmult;
	Caux.M[padsym] = padmult;

	while ( dec.readAlignment() )
	{
		if (
			algn.isMapped() && (!algn.isQCFail()) &&
			algn.getLseq()
		)
		{
			assert ( ! pendinginserts.size() );

			uint32_t const numcigop = algn.getCigarOperations(cigop);
			uint64_t readpos = 0;
			uint64_t refpos = algn.getPos();
			uint64_t const seqlen = algn.decodeRead(bases);
			uint8_t const * qual = libmaus2::bambam::BamAlignmentDecoderBase::getQual(algn.D.begin());

			// handle finished columns
			if ( algn.getRefID() != prevrefid )
			{
				while ( M.size() )
				{
					HeapEntry & H = M.begin()->second;

					if ( outputprefix.size() && (streamRefId != prevrefid) )
					{
						if ( Pstream )
						{
							std::ostringstream fnostr;
							fnostr << outputprefix << "_" << header.getRefIDName(streamRefId);
							libmaus2::aio::OutputStreamInstance PFOS(fnostr.str());
							PFOS << ">" << header.getRefIDName(streamRefId) << '\n';
							PFOS << Pstream->str() << '\n';
//.........这里部分代码省略.........
开发者ID:gt1，项目名称:biobambam2，代码行数:101，代码来源:bamheap2.cpp


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