C++ ArgInfo::getDefaultTmpFileName方法代码示例

uint64_t bamrecompress(libmaus2::util::ArgInfo const & arginfo)
{
	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
	int const numthreads = std::max(1,arginfo.getValue<int>("numthreads",getDefaultNumThreads()));

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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());
		}
	}
	/*
	 * end md5/index callbacks
	 */

	libmaus2::lz::BgzfInflateDeflateParallel::unique_ptr_type BIDP(new libmaus2::lz::BgzfInflateDeflateParallel(std::cin,std::cout,level,numthreads,4*numthreads));

	for ( uint64_t i = 0; i < cbs.size(); ++i )
		BIDP->registerBlockOutputCallback(cbs[i]);

	libmaus2::autoarray::AutoArray<char> B(64*1024,false);
	int r;
	uint64_t t = 0;
	uint64_t last = std::numeric_limits<uint64_t>::max();
	uint64_t lcnt = 0;
	uint64_t const mod = 64*1024*1024;
	libmaus2::timing::RealTimeClock rtc; rtc.start();
	libmaus2::timing::RealTimeClock lrtc; lrtc.start();

	while ( (r = BIDP->read(B.begin(),B.size())) )
	{
		BIDP->write(B.begin(),r);

		lcnt += r;
		t += r;

		if ( t/mod != last/mod )
		{
			if ( verbose )
			{
				if ( isatty(STDERR_FILENO) )
					std::cerr
						<< "\r" << std::string(60,' ') << "\r";

				std::cerr
						<< rtc.formatTime(rtc.getElapsedSeconds()) << " " << t/(1024*1024) << "MB, " << (lcnt/lrtc.getElapsedSeconds())/(1024.0*1024.0) << "MB/s";

				if ( isatty(STDERR_FILENO) )
					std::cerr << std::flush;
				else
					std::cerr << std::endl;
			}

			lrtc.start();
			last = t;
			lcnt = 0;
		}
	}

	if ( verbose )
	{
		if ( isatty(STDERR_FILENO) )
			std::cerr
				<< "\r" << std::string(60,' ') << "\r";
//.........这里部分代码省略.........

int bamclipreinsert(::libmaus2::util::ArgInfo const & arginfo)
{
	if ( isatty(STDIN_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	if ( isatty(STDOUT_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());

	::libmaus2::bambam::BamDecoder dec(std::cin,false);
	::libmaus2::bambam::BamHeader const & header = dec.getHeader();

	std::string const headertext(header.text);

	// add PG line to header
	std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
		headertext,
		"bamclipreinsert", // ID
		"bamclipreinsert", // PN
		arginfo.commandline, // CL
		::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
		std::string(PACKAGE_VERSION) // VN
	);

	// construct new header
	libmaus2::bambam::BamHeader const uphead(upheadtext);

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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;
	/*
	 * end md5/index callbacks
	 */

	::libmaus2::bambam::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,uphead,level,Pcbs));
	libmaus2::bambam::BamAuxFilterVector bafv;
 	// bafv.set('z','z');
 	// std::vector<uint8_t> R(8);
 	// std::string const zz("zz");

	libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
	uint64_t c = 0;

	libmaus2::autoarray::AutoArray < std::pair<uint8_t,uint8_t> > auxtags;
	libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigop;
	std::stack < libmaus2::bambam::cigar_operation > hardstack;
	libmaus2::bambam::BamAlignment::D_array_type Tcigar;
//.........这里部分代码省略.........

int bamreset(::libmaus2::util::ArgInfo const & arginfo)
{
	if ( isatty(STDIN_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	if ( isatty(STDOUT_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
		se.finish();
		throw se;
	}
	
	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
	int const resetsortorder = arginfo.getValue<int>("resetsortorder",getDefaultResetSortOrder());
	
	::libmaus2::bambam::BamDecoder dec(std::cin,false);
	::libmaus2::bambam::BamHeader const & header = dec.getHeader();

	std::string headertext = header.text;

	// no replacement header file given
	if ( ! arginfo.hasArg("resetheadertext") )
	{
		// remove SQ lines
		std::vector<libmaus2::bambam::HeaderLine> allheaderlines = libmaus2::bambam::HeaderLine::extractLines(headertext);

		std::ostringstream upheadstr;
		for ( uint64_t i = 0; i < allheaderlines.size(); ++i )
			if ( allheaderlines[i].type != "SQ" )
				upheadstr << allheaderlines[i].line << std::endl;

		headertext = upheadstr.str();
	}
	// replace header given in file
	else
	{
		std::string const headerfilename = arginfo.getUnparsedValue("resetheadertext","");
		uint64_t const headerlen = libmaus2::util::GetFileSize::getFileSize(headerfilename);
		libmaus2::aio::CheckedInputStream CIS(headerfilename);
		libmaus2::autoarray::AutoArray<char> ctext(headerlen,false);
		CIS.read(ctext.begin(),headerlen);
		headertext = std::string(ctext.begin(),ctext.end());		
	}

	// add PG line to header
	headertext = libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
		headertext,
		"bamreset", // ID
		"bamreset", // PN
		arginfo.commandline, // CL
		::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
		std::string(PACKAGE_VERSION) // VN			
	);
	
	// construct new header
	libmaus2::bambam::BamHeader uphead(headertext);
	if ( resetsortorder )
		uphead.changeSortOrder("unknown");

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	std::string const tmpfileindex = tmpfilenamebase + "_index";
	::libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfileindex);
	uint32_t const excludeflags = libmaus2::bambam::BamFlagBase::stringToFlags(
		arginfo.getValue<std::string>("exclude",getDefaultExcludeFlags()));

	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
	{
		if ( arginfo.hasArg("indexfilename") &&  arginfo.getUnparsedValue("indexfilename","") != "" )
			indexfilename = arginfo.getUnparsedValue("indexfilename","");
		else
//.........这里部分代码省略.........

int bam12auxmerge(::libmaus2::util::ArgInfo const & arginfo)
{
	if ( isatty(STDIN_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing to read binary data from terminal, please redirect standard input to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	if ( isatty(STDOUT_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	std::string const prefilename = arginfo.getRestArg<std::string>(0);
	libmaus2::bambam::BamDecoder bampredec(prefilename);

	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
	int const ranksplit = arginfo.getValue<int>("ranksplit",getDefaultRankSplit());
	int const rankstrip = arginfo.getValue<int>("rankstrip",getDefaultRankSplit());
	int const clipreinsert = arginfo.getValue<int>("clipreinsert",getDefaultClipReinsert());
	int const zztoname = arginfo.getValue<int>("zztoname",getDefaultZZToName());
	int const sanity = arginfo.getValue<int>("sanity",getDefaultSanity());
	uint64_t const mod = arginfo.getValue<int>("mod",getDefaultMod());
	uint64_t const bmod = libmaus2::math::nextTwoPow(mod);
	uint64_t const bmask = bmod-1;

	libmaus2::autoarray::AutoArray<char> Aread;

	::libmaus2::bambam::BamDecoder bamdec(std::cin,false);
	::libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
	::libmaus2::bambam::BamHeader const & preheader = bampredec.getHeader();

	std::string const headertext(header.text);
	std::string const preheadertext(libmaus2::bambam::HeaderLine::removeSequenceLines(preheader.text));

	libmaus2::bambam::ProgramHeaderLineSet headerlines(headertext);
	libmaus2::bambam::ProgramHeaderLineSet preheaderlines(preheadertext);

	std::vector<libmaus2::bambam::HeaderLine> allheaderlines = libmaus2::bambam::HeaderLine::extractLines(headertext);

	std::string const lastid = preheaderlines.getLastIdInChain();

	std::stack < std::pair<uint64_t,std::string> > pgtodo;
	for ( uint64_t i = 0; i < headerlines.roots.size(); ++i )
		pgtodo.push(std::pair<uint64_t,std::string>(headerlines.roots[i],lastid));

	std::string upheadtext = preheadertext;
	while ( pgtodo.size() )
	{
		uint64_t const hid = pgtodo.top().first;
		std::string const PP = pgtodo.top().second;
		pgtodo.pop();
		libmaus2::bambam::HeaderLine const & line = headerlines.lines[hid];

		// ID, PP, PN, CL, VN
		std::string       ID = (line.M.find("ID") != line.M.end()) ? line.M.find("ID")->second : "";
		std::string const PN = (line.M.find("PN") != line.M.end()) ? line.M.find("PN")->second : "";
		std::string const CL = (line.M.find("CL") != line.M.end()) ? line.M.find("CL")->second : "";
		std::string const VN = (line.M.find("VN") != line.M.end()) ? line.M.find("VN")->second : "";

		upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLineRef(
			upheadtext,
			ID,
			PN,
			CL,
			PP,
			VN
		);

		if ( headerlines.edges.find(hid) != headerlines.edges.end() )
		{
			std::vector<uint64_t> const & children = headerlines.edges.find(hid)->second;

			for ( uint64_t j = 0; j < children.size(); ++j )
				pgtodo.push(std::pair<uint64_t,std::string>(children[j],ID));
		}
	}

	/* copy SQ lines */
	std::ostringstream sqconcstr;
	sqconcstr << upheadtext;
	for ( uint64_t i = 0; i < allheaderlines.size(); ++i )
		if ( allheaderlines[i].type == "SQ" )
			sqconcstr << allheaderlines[i].line << "\n";
	upheadtext = sqconcstr.str();

	::libmaus2::bambam::BamHeader uphead(upheadtext);
	uphead.changeSortOrder("unknown");

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	std::string const tmpfileindex = tmpfilenamebase + "_index";
//.........这里部分代码省略.........

uint64_t bamheaderfilter(libmaus2::util::ArgInfo const & arginfo)
{
	std::string const inputfilename = arginfo.getUnparsedValue("I","");

	if ( ! inputfilename.size() || inputfilename == "-" )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "No input filename given, please set the I key appropriately." << std::endl;
		se.finish();
		throw se;
	}

	libmaus2::bitio::IndexedBitVector::unique_ptr_type usedrefseq;
	libmaus2::bitio::IndexedBitVector::unique_ptr_type usedrg;
	libmaus2::bambam::BamHeader::unique_ptr_type uheader;

	getUsedRefSeqs(arginfo,usedrefseq,usedrg,uheader);

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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());
		}
	}
	/*
	 * end md5/index callbacks
	 */

	std::string headertext(uheader->text);
	std::vector<libmaus2::bambam::HeaderLine> hl = libmaus2::bambam::HeaderLine::extractLines(headertext);
	
	std::ostringstream headertextostr;
	uint64_t rscnt = 0;
	uint64_t rgcnt = 0;
	for ( uint64_t i = 0; i < hl.size(); ++i )
	{
		if ( hl[i].type == "SQ" )
		{
			if ( usedrefseq->get(rscnt) )
				headertextostr << hl[i].line << std::endl;

			rscnt += 1;
		}
		else if ( hl[i].type == "RG" )
		{
			if ( usedrg->get(rgcnt) )
				headertextostr << hl[i].line << std::endl;
			
			rgcnt += 1;
		}
		else
		{
			headertextostr << hl[i].line << std::endl;
		}
	}
	headertext = headertextostr.str();

	// add PG line to header
	std::string const upheadtext = ::libmaus2::bambam::ProgramHeaderLineSet::addProgramLine(
		headertext,
		"bamheaderfilter", // ID
		"bamheaderfilter", // PN
		arginfo.commandline, // CL
		::libmaus2::bambam::ProgramHeaderLineSet(headertext).getLastIdInChain(), // PP
		std::string(PACKAGE_VERSION) // VN			
//.........这里部分代码省略.........

int bammaskflags(::libmaus2::util::ArgInfo const & arginfo)
{
	uint64_t const maskpos = arginfo.getValue<uint64_t>("maskpos",0xFFFFUL);
	uint64_t const maskneg = arginfo.getValue<uint64_t>("maskneg",getDefaultMaskNeg());
	uint64_t const mask = maskpos & (~maskneg);

	if ( mask )
	{
		std::cerr << "Keeping flags ";
		for ( uint64_t i = 1; i <= ::libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FSUPPLEMENTARY; i <<= 1 )
			if ( mask & i )
				std::cerr << static_cast< ::libmaus2::bambam::BamFlagBase::bam_flags >(i) << ";";
		std::cerr << std::endl;
		std::cerr << "Erasing flags ";
		for ( uint64_t i = 1; i <= ::libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FSUPPLEMENTARY; i <<= 1 )
			if ( !(mask & i) )
				std::cerr << static_cast< ::libmaus2::bambam::BamFlagBase::bam_flags >(i) << ";";
		std::cerr << std::endl;
	}
	else
	{
		std::cerr << "Erasing all flags." << std::endl;
	}

	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const resetmatecoord = arginfo.getValue<int>("resetmatecoord",0);

	::libmaus2::bambam::BamDecoder BD(std::cin);
	::libmaus2::bambam::BamHeader const & bamheader = BD.getHeader();

	std::string const headertext(bamheader.text);

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

	::libmaus2::bambam::BamAlignment & alignment = BD.getAlignment();

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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;
	/*
	 * end md5/index callbacks
	 */

	::libmaus2::bambam::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,uphead,level,Pcbs));

	while ( BD.readAlignment() )
	{
		alignment.putFlags(alignment.getFlags() & mask);
		if ( resetmatecoord )
//.........这里部分代码省略.........

int bamrecalculatecigar(libmaus2::util::ArgInfo const & arginfo)
{
	if ( isatty(STDOUT_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
	// input decoder wrapper
	libmaus2::bambam::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
		libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
			arginfo,false // put rank
		)
	);

	libmaus2::bambam::BamAlignmentDecoder & bamdec = decwrapper->getDecoder();
	libmaus2::bambam::BamAlignment & algn = bamdec.getAlignment();
	libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
	::libmaus2::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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;
	/*
	 * end md5/index callbacks
	 */

	libmaus2::bambam::BamBlockWriterBase::unique_ptr_type writer(
		libmaus2::bambam::BamBlockWriterBaseFactory::construct(*uphead, arginfo, Pcbs)
	);

	libmaus2::autoarray::AutoArray<libmaus2::bambam::cigar_operation> cigopin;
	libmaus2::autoarray::AutoArray<char> readdata;
	libmaus2::bambam::BamAlignment::D_array_type T;

	if ( ! arginfo.hasArg("reference") )
	{
		libmaus2::exception::LibMausException se;
		se.getStream() << "reference key is missing." << std::endl;
		se.finish();
		throw se;
	}

	std::string const reference = arginfo.getUnparsedValue("reference","");

	if ( ! libmaus2::util::GetFileSize::fileExists(reference) )
	{
		libmaus2::exception::LibMausException se;
		se.getStream() << "file " << reference << " does not exist." << std::endl;
		se.finish();
		throw se;
	}

	libmaus2::fastx::FastAIndex::unique_ptr_type FAindex(libmaus2::fastx::FastAIndex::load(reference + ".fai"));
	libmaus2::aio::InputStreamInstance FAISI(reference);

//.........这里部分代码省略.........

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.........

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.........

int bamfilterflags(::libmaus2::util::ArgInfo const & arginfo)
{
	uint32_t const excludeflags = libmaus2::bambam::BamFlagBase::stringToFlags(arginfo.getValue<std::string>("exclude",""));

	std::cerr << "[V] excluding " << excludeflags << std::endl;

	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",Z_DEFAULT_COMPRESSION));
	
	uint64_t const numthreads = arginfo.getValue<uint64_t>("numthreads",1);
	uint64_t cnt = 0;
	uint64_t kept = 0;

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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;
	/*
	 * end md5/index callbacks
	 */
	 

	if ( numthreads == 1 )
	{
		::libmaus2::bambam::BamDecoder BD(std::cin);
		::libmaus2::bambam::BamHeader const & bamheader = BD.getHeader();
		::libmaus2::bambam::BamHeader::unique_ptr_type uphead(libmaus2::bambam::BamHeaderUpdate::updateHeader(arginfo,bamheader,"bamfilterflags",std::string(PACKAGE_VERSION)));
		::libmaus2::bambam::BamAlignment & alignment = BD.getAlignment();
		::libmaus2::bambam::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,*uphead,level,Pcbs));
	
		for ( ; BD.readAlignment(); ++cnt )
		{
			if ( cnt % (1024*1024) == 0 )
				std::cerr << "[V] processed " << cnt << " kept " << kept << " removed " << (cnt-kept) << std::endl;
			if ( ! (alignment.getFlags() & excludeflags) )			
			{
				alignment.serialise(writer->getStream());
				++kept;
			}
		}

		std::cerr << "[V] " << cnt << std::endl;	
	}
	else
	{
		::libmaus2::bambam::BamHeaderUpdate UH(arginfo,"bamfilterflags",std::string(PACKAGE_VERSION));
		libmaus2::bambam::BamParallelRewrite BPR(std::cin,UH,std::cout,Z_DEFAULT_COMPRESSION,numthreads,4 /* blocks per thread */,Pcbs);
		libmaus2::bambam::BamAlignmentDecoder & dec = BPR.getDecoder();
		libmaus2::bambam::BamParallelRewrite::writer_type & writer = BPR.getWriter();

		libmaus2::bambam::BamAlignment const & algn = dec.getAlignment();
		for ( ; dec.readAlignment(); ++cnt )
		{
			if ( cnt % (1024*1024) == 0 )
				std::cerr << "[V] processed " << cnt << " kept " << kept << " removed " << (cnt-kept) << std::endl;
			if ( ! (algn.getFlags() & excludeflags) )
			{
				algn.serialise(writer.getStream());	
				++kept;
			}
		}
//.........这里部分代码省略.........

int bamcat(libmaus2::util::ArgInfo const & arginfo)
{
	if ( isatty(STDOUT_FILENO) )
	{
		::libmaus2::exception::LibMausException se;
		se.getStream() << "Refusing write binary data to terminal, please redirect standard output to pipe or file." << std::endl;
		se.finish();
		throw se;
	}

	int const level = libmaus2::bambam::BamBlockWriterBaseFactory::checkCompressionLevel(arginfo.getValue<int>("level",getDefaultLevel()));
	int const verbose = arginfo.getValue<int>("verbose",getDefaultVerbose());
	int const streaming = arginfo.getValue<int>("streaming",getDefaultStreaming());

	std::vector<std::string> inputfilenames = arginfo.getPairValues("I");
	
	for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
		inputfilenames.push_back(arginfo.restargs[i]);
	
	libmaus2::bambam::BamCat bamdec(inputfilenames, false /* put rank */, streaming);
	libmaus2::bambam::BamAlignment const & algn = bamdec.getAlignment();
	libmaus2::bambam::BamHeader const & header = bamdec.getHeader();
	::libmaus2::bambam::BamHeader::unique_ptr_type uphead(updateHeader(arginfo,header));

	/*
	 * start index/md5 callbacks
	 */
	std::string const tmpfilenamebase = arginfo.getValue<std::string>("tmpfile",arginfo.getDefaultTmpFileName());
	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 ( 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());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	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;
	/*
	 * end md5/index callbacks
	 */


	::libmaus2::bambam::BamWriter::unique_ptr_type writer(new ::libmaus2::bambam::BamWriter(std::cout,*uphead,level,Pcbs));
	libmaus2::bambam::BamWriter::stream_type & bamoutstr = writer->getStream();
	if ( verbose )
	{
		uint64_t c = 0;
		while ( bamdec.readAlignment() )
		{
			algn.serialise(bamoutstr);
			
			if ( ((++c) & ((1ull<<20)-1)) == 0 )
				std::cerr << "[V] " << c << std::endl;
		}
		
		std::cerr << "[V] " << c << std::endl;
	}
	else
		while ( bamdec.readAlignment() )
			algn.serialise(bamoutstr);

	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
//.........这里部分代码省略.........

static std::string getDefaultFilePrefix(::libmaus2::util::ArgInfo const & arginfo) { return arginfo.getDefaultTmpFileName(); }

static int call_damapper(libmaus2::util::ArgParser const & arg, libmaus2::util::ArgInfo const & arginfo)
{
	unsigned int const damapper_arg_k = arg.uniqueArgPresent("k") ? arg.getUnsignedNumericArg<uint64_t>("k") : 20;
	         int const damapper_arg_t = arg.uniqueArgPresent("t") ? arg.getParsedArg<int>("t") : -1;
	         int const damapper_arg_M = arg.uniqueArgPresent("M") ? arg.getParsedArg<int>("M") : -1;
	double const damapper_arg_e = arg.uniqueArgPresent("e") ? arg.getParsedArg<double>("e") : std::numeric_limits<double>::min();
	         int const damapper_arg_s = arg.uniqueArgPresent("s") ? arg.getParsedArg<int>("s") : -1;
	double const damapper_arg_n = arg.uniqueArgPresent("n") ? arg.getParsedArg<double>("n") : std::numeric_limits<double>::min();
	         int const damapper_arg_B = arg.uniqueArgPresent("B") ? arg.getParsedArg<int>("B") : -1;
	         int const damapper_arg_T = arg.uniqueArgPresent("T") ? arg.getParsedArg<int>("T") : -1;
	         int const damapper_arg_b = arg.uniqueArgPresent("b") ? 1 :  0; // comp bias
	         int const damapper_arg_v = arg.uniqueArgPresent("v") ? 1 :  0; // verbose
	         int const damapper_arg_p = arg.uniqueArgPresent("p") ? 1 :  0; // repeat profile (not used)

	unsigned int const numthreads = damapper_arg_T < 0 ? 4 : damapper_arg_T;

	unsigned int const refblocksize = arg.uniqueArgPresent("refblocksize") ? arg.getUnsignedNumericArg<uint64_t>("refblocksize") : 250;
	unsigned int const readblocksize = arg.uniqueArgPresent("readblocksize") ? arg.getUnsignedNumericArg<uint64_t>("readblocksize") : 250;

	std::string const argindexdir = arg.uniqueArgPresent("I") ? arg["I"] :  std::string();
	std::string const argworkdir = arg.uniqueArgPresent("W") ? arg["W"] :  std::string();
	std::string const workdir = makeAbsolute(argworkdir.size() ? argworkdir : ".");

	mkdirP(workdir);

	unsigned int const fastacolwidth = 80;
	bool const reformatref = true;
	bool const reformatreads = true;

	std::string progname = arg.progname;
	ProgramDescriptor PD_fasta2DAM("fasta2DAM",progname);
	ProgramDescriptor PD_DBsplit("DBsplit",progname);
	ProgramDescriptor PD_HPC_damapper("HPC.damapper",progname);
	ProgramDescriptor PD_damapper("damapper",progname);
	ProgramDescriptor PD_lascat("lascat",progname);
	ProgramDescriptor PD_laschainsort("laschainsort",progname);
	ProgramDescriptor PD_lastobam("lastobam",progname);
	ProgramDescriptor PD_LAsort("LAsort",progname);
	ProgramDescriptor PD_LAcat("LAcat",progname);
	ProgramDescriptor PD_LAmerge("LAmerge",progname);

	std::vector<std::string> Vpathadd;
	Vpathadd.push_back(PD_LAsort.dir);
	Vpathadd.push_back(PD_LAcat.dir);
	Vpathadd.push_back(PD_LAmerge.dir);
	std::sort(Vpathadd.begin(),Vpathadd.end());
	Vpathadd.resize ( std::unique(Vpathadd.begin(),Vpathadd.end()) - Vpathadd.begin() );

	std::ostringstream npathstr;
	npathstr << getenv("PATH");
	for ( uint64_t i = 0; i < Vpathadd.size(); ++i )
		npathstr << ":" << Vpathadd[i];
	std::string const npath = npathstr.str();
	libmaus2::util::WriteableString Wnpath(npath);
	setenv("PATH",Wnpath.A.begin(),1 /* overwrite */);

	std::string const reffn = arg[0];

	if ( ! libmaus2::util::GetFileSize::fileExists(reffn) )
	{
		libmaus2::exception::LibMausException lme;
		lme.getStream() << "call.damapper: reference file " << reffn << " does not exist" << std::endl;
		lme.finish();
		throw lme;
	}

	static char const * faend[] = { ".fasta",".fa",0 };

	std::string const refdir = sdirname(reffn);
	std::string const indexdir = makeAbsolute(argindexdir.size() ? argindexdir : refdir);
	std::string const reffile = sbasename(reffn);
	std::string const reffileclipped = libmaus2::util::OutputFileNameTools::endClip(reffile,&faend[0]);

	mkdirP(indexdir);

	std::string const refdam = indexdir + "/"  + reffileclipped + ".dam";
	std::string const refidx = indexdir + "/." + reffileclipped + ".idx";
	std::string const refhdr = indexdir + "/." + reffileclipped + ".hdr";
	std::string const refbps = indexdir + "/." + reffileclipped + ".bps";
	std::string const indexfasta = indexdir + "/"  + reffileclipped + ".dam.fasta";

	if (
		! libmaus2::util::GetFileSize::fileExists(refdam) || libmaus2::util::GetFileSize::isOlder(refdam,reffn) ||
		! libmaus2::util::GetFileSize::fileExists(refidx) || libmaus2::util::GetFileSize::isOlder(refidx,reffn) ||
		! libmaus2::util::GetFileSize::fileExists(refhdr) || libmaus2::util::GetFileSize::isOlder(refhdr,reffn) ||
		! libmaus2::util::GetFileSize::fileExists(refbps) || libmaus2::util::GetFileSize::isOlder(refbps,reffn) ||
		! libmaus2::util::GetFileSize::fileExists(indexfasta) || libmaus2::util::GetFileSize::isOlder(indexfasta,reffn)
	)
	{
		std::string const tmpbase = arginfo.getDefaultTmpFileName();
		std::string const reffastatmp  = indexdir + "/"  + tmpbase + ".fasta";
		std::string const refdamtmp    = indexdir + "/"  + tmpbase + ".dam";
		std::string const refdamidxtmp = indexdir + "/." + tmpbase + ".idx";
		std::string const refdamhdrtmp = indexdir + "/." + tmpbase + ".hdr";
		std::string const refdambpstmp = indexdir + "/." + tmpbase + ".bps";

		libmaus2::util::TempFileRemovalContainer::addTempFile(refdamtmp);
		libmaus2::util::TempFileRemovalContainer::addTempFile(refdamidxtmp);
		libmaus2::util::TempFileRemovalContainer::addTempFile(refdamhdrtmp);
		libmaus2::util::TempFileRemovalContainer::addTempFile(refdambpstmp);
//.........这里部分代码省略.........