Esempio n. 1
0
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";

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

		std::cerr << std::endl;
	}

	BIDP.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return 0;
}
Esempio n. 2
0
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;
	libmaus2::bambam::BamAuxFilterVector auxfilterout;
	auxfilterout.set('q','s');
	auxfilterout.set('q','q');

	while ( dec.readAlignment() )
	{
		// reinsert clipped parts and attach soft clipping cigar operations as needed
		clipReinsert(algn,auxtags,bafv,cigop,Tcigar,hardstack,auxfilterout);

		algn.serialise(writer->getStream());

		++c;

		if ( verbose && (c & (1024*1024-1)) == 0 )
 			std::cerr << "[V] " << c/(1024*1024) << std::endl;
	}

	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 3
0
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
			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::timing::RealTimeClock rtc; rtc.start();
 	
	libmaus2::bambam::BamAlignment & algn = dec.getAlignment();
	uint64_t c = 0;

	bool const resetaux = arginfo.getValue<int>("resetaux",getDefaultResetAux());
	libmaus2::bambam::BamAuxFilterVector::unique_ptr_type const prgfilter(libmaus2::bambam::BamAuxFilterVector::parseAuxFilterList(arginfo));
	libmaus2::bambam::BamAuxFilterVector const * rgfilter = prgfilter.get();

	while ( dec.readAlignment() )
	{
		bool const keep = resetAlignment(algn,resetaux /* reset aux */,excludeflags,rgfilter);
		
		if ( keep )
			algn.serialise(writer->getStream());

		if ( verbose && (++c & (1024*1024-1)) == 0 )
 			std::cerr << "[V] " << c/(1024*1024) << " " << (c / rtc.getElapsedSeconds()) << std::endl;
	}
	
	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 4
0
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";
	::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::BamAlignment & algn = bamdec.getAlignment();
	::libmaus2::bambam::BamAlignment & prealgn = bampredec.getAlignment();
	int64_t curid = -1;

	libmaus2::autoarray::AutoArray< std::pair<uint8_t,uint8_t> > auxpre;
	libmaus2::autoarray::AutoArray< std::pair<uint8_t,uint8_t> > auxnew;

	libmaus2::bambam::BamAuxFilterVector auxfilter;

	// helpers for clipReinsert
	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;
	libmaus2::bambam::BamAuxFilterVector bafv;
	libmaus2::bambam::BamAuxFilterVector auxfilterout;
	auxfilterout.set('q','s');
	auxfilterout.set('q','q');

	// helpers for zztoname
 	libmaus2::bambam::BamAuxFilterVector zzbafv;
 	zzbafv.set('z','z');

    	// tag filters for secondary/supplementary reads
	libmaus2::bambam::BamAuxFilterVector auxfiltersec;

	auxfiltersec.set('q','s');
	auxfiltersec.set('q','q');
	auxfiltersec.set('a','s');
	auxfiltersec.set('a','h');
	auxfiltersec.set('a','a');
	auxfiltersec.set('a','f');
	auxfiltersec.set('a','r');
	auxfiltersec.set('a','3');

	// loop over aligned BAM file
	while ( bamdec.readAlignment() )
	{
		if ( ranksplit )
			split12(algn);

		// extract rank
		char const * name = algn.getName();
		char const * u1 = name;
		bool ok = true;
		uint64_t rank = 0;
		while ( *u1 && *u1 != '_' )
		{
			rank *= 10;
			rank += (*u1-'0');
			ok = ok && isdigit(*u1);
			++u1;
		}

		// unable to find rank?	write out as is and continue
		if ( ! ok )
		{
			algn.serialise(writer->getStream());
			continue;
		}

		// loop over unaligned BAM file
		while ( curid != static_cast<int64_t>(rank) )
		{
			bool const a_ok = bampredec.readAlignment();

			if ( ! a_ok )
			{
				libmaus2::exception::LibMausException se;
				se.getStream() << "Found unexpected EOF on file " << prefilename << std::endl;
				se.finish();
				throw se;
			}
			assert ( a_ok );
			++curid;

			if ( verbose && (! (curid & bmask)) )
				std::cerr << "[V] " << (curid / bmod) << std::endl;
		}

		if ( verbose > 1 )
			std::cerr << "Merging:\n" << algn.formatAlignment(header) << "\n" << prealgn.formatAlignment(preheader) << std::endl;

		uint64_t pretagnum = prealgn.enumerateAuxTags(auxpre);
		uint64_t newtagnum = algn.enumerateAuxTags(auxnew);

		// do some sanity checking
		if ( sanity )
		{
		    	// first do a name check
			char const * prename = prealgn.getName();
			u1++; // put on the first letter of readname

			if ( verbose > 1 )
    	    	    	    	std::cerr << "Sanity: comparing " << name << " and " << prename << std::endl;

			if ( !is_suffix(prename, u1) ) // names do not match
			{
			    	libmaus2::exception::LibMausException se;
			    	se.getStream() << "Sanity check failed on read names, found " << name << " and " << prename << std::endl;
				se.finish();
				throw se;
			}

			// now the names match so try the flags

			if ( !(algn.isPaired() == prealgn.isPaired() &&
			     algn.isRead1() == prealgn.isRead1() &&
			     algn.isRead2() == prealgn.isRead2()) )
			{
			    	libmaus2::exception::LibMausException se;
				se.getStream() << "Sanity check failed on flags, " << std::endl
				    	       << "Aligned " << name << " paired " << algn.isPaired() << " first " << algn.isRead1() << " last " << algn.isRead2() << std::endl
			    	    	       << "Unaligned " << prename << " paired " << prealgn.isPaired() << " first " << prealgn.isRead1() << " last " << prealgn.isRead2() << std::endl;
				se.finish();
				throw se;
			}

			if ( verbose > 1 )
			    std::cerr << "Sanity check on flags: " << std::endl
				    	       << "Aligned " << name << " paired " << algn.isPaired() << " first " << algn.isRead1() << " last " << algn.isRead2() << std::endl
			    	    	       << "Unaligned " << prename << " paired " << prealgn.isPaired() << " first " << prealgn.isRead1() << " last " << prealgn.isRead2() << std::endl;


		}

		std::sort(auxpre.begin(),auxpre.begin()+pretagnum);
		std::sort(auxnew.begin(),auxnew.begin()+newtagnum);

		if ( verbose > 1 )
			std::cerr << "pretagnum=" << pretagnum << " newtagnum=" << newtagnum << std::endl;

		std::pair<uint8_t,uint8_t> * prec = auxpre.begin();
		std::pair<uint8_t,uint8_t> * pree = prec + pretagnum;
		std::pair<uint8_t,uint8_t> * preo = prec;

		std::pair<uint8_t,uint8_t> * newc = auxnew.begin();
		std::pair<uint8_t,uint8_t> * newe = newc + newtagnum;
		std::pair<uint8_t,uint8_t> * newo = newc;

		while ( prec != pree && newc != newe )
		{
			// pre which is not in new
			if ( *prec < *newc )
			{
				*(preo++) = *(prec++);
			}
			// tag in both, drop pre
			else if ( *prec == *newc )
			{
				*(newo++) = *(newc++);
				prec++;
			}
			// new not in pre
			else
			{
				*(newo++) = *(newc++);
			}
		}

		while ( prec != pree )
			*(preo++) = *(prec++);
		while ( newc != newe )
			*(newo++) = *(newc++);

		pretagnum = preo-auxpre.begin();
		newtagnum = newo-auxnew.begin();

		for ( uint64_t i = 0; i < pretagnum; ++i )
			auxfilter.set(auxpre[i].first,auxpre[i].second);

		algn.copyAuxTags(prealgn, auxfilter);

		for ( uint64_t i = 0; i < pretagnum; ++i )
			auxfilter.clear(auxpre[i].first,auxpre[i].second);

		if ( verbose > 1 )
		{
			std::cerr << "pretagnum=" << pretagnum << " newtagnum=" << newtagnum << std::endl;
			std::cerr << "result: " << algn.formatAlignment(header) << std::endl;
		}


		if ( algn.isSecondary() || algn.isSupplementary() )
		{
		    	// adding adapter clip data to secondary/supplementary reads
			// can lead to incorrect clip reinserts so remove these tags

			algn.filterOutAux(auxfiltersec);
		}


		// copy QC fail flag from original file to aligner output
		if ( prealgn.isQCFail() )
			algn.putFlags( algn.getFlags() | libmaus2::bambam::BamFlagBase::LIBMAUS2_BAMBAM_FQCFAIL );

		if ( rankstrip )
			strip12(algn);

		if ( clipreinsert )
			clipReinsert(algn,auxtags,bafv,cigop,Tcigar,hardstack,auxfilterout);

		if ( zztoname )
			zzToRank(algn,zzbafv);

		algn.serialise(writer->getStream());
	}

	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 5
0
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			
	);
	// construct new header
	::libmaus2::bambam::BamHeader uphead(upheadtext);
	libmaus2::bambam::BamBlockWriterBase::unique_ptr_type Pout ( libmaus2::bambam::BamBlockWriterBaseFactory::construct(uphead, arginfo, &cbs) );

	// input decoder wrapper
	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::BamAlignment & algn = dec.getAlignment();
	
	while ( dec.readAlignment() )
	{
		if ( (!algn.isPaired()) && algn.isMapped() )
		{
			assert ( algn.getRefID() >= 0 );
			assert ( algn.getRefID() < static_cast<int64_t>(usedrefseq->size()) );
			assert ( usedrefseq->get(algn.getRefID()) );
			assert ( usedrefseq->rank1(algn.getRefID())-1 < uphead.getNumRef() );
			algn.putRefId(usedrefseq->rank1(algn.getRefID())-1);
		}
		if ( algn.isPaired() && algn.isMapped() )
		{
			assert ( algn.getRefID() >= 0 );
			assert ( algn.getRefID() < static_cast<int64_t>(usedrefseq->size()) );
			assert ( usedrefseq->get(algn.getRefID()) );
			assert ( usedrefseq->rank1(algn.getRefID())-1 < uphead.getNumRef() );
			algn.putRefId(usedrefseq->rank1(algn.getRefID())-1);
		}
		if ( algn.isPaired() && algn.isMateMapped() )
		{
			assert ( algn.getNextRefID() >= 0 );
			assert ( algn.getNextRefID() < static_cast<int64_t>(usedrefseq->size()) );
			assert ( usedrefseq->get(algn.getNextRefID()) );
			assert ( usedrefseq->rank1(algn.getNextRefID())-1 < uphead.getNumRef() );
			algn.putNextRefId(usedrefseq->rank1(algn.getNextRefID())-1);
		}
		
		// erase unmapped refid and pos
		if ( algn.isUnmap() )
		{
			algn.putRefId(-1);
			algn.putPos(-1);
		}
		if ( algn.isMateUnmap() )
		{
			algn.putNextRefId(-1);
			algn.putNextPos(-1);
		}

		Pout->writeAlignment(algn);
	}


	Pout.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}
	
	return 0;
}
Esempio n. 6
0
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 )
		{
			alignment.putNextRefId(-1);
			alignment.putNextPos(-1);
		}
		alignment.serialise(writer->getStream());
	}

	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 7
0
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 )
			{
				uint64_t const l = algn.getLseq();
				uint8_t const * Qc = libmaus2::bambam::BamAlignmentDecoderBase::getQual(algn.D.begin());
				uint8_t const * const Qe = Qc + l;

				while ( Qc != Qe )
					H[*(Qc++)]++;
			}

			uint64_t const lname = algn.getLReadName();
			char const * name = algn.getName();
			std::copy(name,name+lname+1,lastvalidname.begin());

			alsok += 1;
		}
	}
	catch(std::exception const & ex)
	{
		std::cerr << "[E] name of last valid alignment was " << lastvalidname.begin() << std::endl;
		std::cerr << "[E] read " << alsok << " valid alignments" << std::endl;
		throw;
	}

	Pout.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	if ( verbose )
		std::cerr << "[V] checked " << alsok << " alignments in " << rtc.formatTime(rtc.getElapsedSeconds())
			<< " (" << alsok / rtc.getElapsedSeconds() << " al/s)" << std::endl;

	if ( basequalhist )
	{
		uint64_t const s = std::accumulate(H.begin(),H.end(),0ull);

		uint64_t a = 0;
		uint64_t minq = std::numeric_limits<uint64_t>::max();
		uint64_t maxq = 0;

		for ( uint64_t i = 0; i < H.size(); ++i )
			if ( H[i] )
			{
				minq = std::min(minq,i);
				maxq = std::max(maxq,i);

				a += H[i];

				std::cerr
					<< "[H]\t" << i << "\t";

				if ( ( static_cast<uint64_t>(i+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(i+33)) )
					std::cerr << static_cast<char>(i+33);

				std::cerr << "\t"
					<< H[i] << "\t"
					<< (H[i] / static_cast<double>(s)) << "\t"
					<< (a / static_cast<double>(s))
					<< std::endl;
			}

		if ( s )
		{
			std::cerr << "[H]\tmin\t" << minq << "\t";
			if ( ( static_cast<uint64_t>(minq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(minq+33)) )
				std::cerr << static_cast<char>(minq+33);
			std::cerr << std::endl;
			std::cerr << "[H]\tmax\t" << maxq << "\t";
			if ( ( static_cast<uint64_t>(maxq+33) < static_cast<uint64_t>(std::numeric_limits<char>::max()) && isprint(maxq+33)) )
				std::cerr << static_cast<char>(maxq+33);
			std::cerr << std::endl;
		}
	}

	return EXIT_SUCCESS;
}
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);

	uint64_t c = 0;
	libmaus2::autoarray::AutoArray<char> ref;
	int64_t refloaded = -1;

	while ( bamdec.readAlignment() )
	{
		if ( algn.isMapped() )
		{
			assert ( algn.getRefID() >= 0 );
			if ( algn.getRefID() != refloaded )
			{
				if ( algn.getRefID() < refloaded )
				{
					libmaus2::exception::LibMausException lme;
					lme.getStream() << "bamrecalculatecigar: file is not sorted by coordinate" << std::endl;
					lme.finish();
					throw lme;
				}

				ref = FAindex->readSequence(FAISI,algn.getRefID());
				refloaded = algn.getRefID();
			}

			uint64_t const numcig = libmaus2::bambam::BamAlignmentDecoderBase::recalculateCigar(
				algn.D.begin(),
				ref.begin() + algn.getPos(),
				cigopin,
				readdata
			);
			algn.replaceCigarString(cigopin,numcig,T);
		}

		writer->writeAlignment(algn);

		if ( ((++c) & ((1ull<<20)-1)) == 0 && verbose )
			std::cerr << "[V] " << c << std::endl;
	}

	if ( verbose )
		std::cerr << "[V] " << c << std::endl;

	writer.reset();

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 9
0
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;
			}
		}
		
		std::cerr << "[V] " << cnt << std::endl;	
	}
	
	std::cerr << "[V] kept " << kept << " removed " << cnt-kept << std::endl;

	if ( Pmd5cb )
	{
		Pmd5cb->saveDigestAsFile(md5filename);
	}
	if ( Pindex )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}
Esempio n. 10
0
int fagzToCompact4(libmaus2::util::ArgInfo const & arginfo)
{
	bool const rc = arginfo.getValue<unsigned int>("rc",1);
	bool const gz = arginfo.getValue<unsigned int>("gz",1);

	std::vector<std::string> inputfilenames;
	inputfilenames = arginfo.restargs;

	if ( arginfo.hasArg("inputfilenames") )
	{
		std::string const inf = arginfo.getUnparsedValue("inputfilenames",std::string());
		libmaus2::aio::InputStream::unique_ptr_type Pinf(libmaus2::aio::InputStreamFactoryContainer::constructUnique(inf));
		while ( *Pinf )
		{
			std::string line;
			std::getline(*Pinf,line);
			if ( line.size() )
				inputfilenames.push_back(line);
		}
	}

	std::string const inlcp = libmaus2::util::OutputFileNameTools::lcp(inputfilenames);
	std::string defout = inlcp;
	defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".gz");
	defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".fasta");
	defout = libmaus2::util::OutputFileNameTools::clipOff(defout,".fa");

	std::string const outputfilename = arginfo.getUnparsedValue("outputfilename",defout + ".compact");
	std::string const metaoutputfilename = outputfilename + ".meta";
	int const verbose = arginfo.getValue<int>("verbose",1);
	libmaus2::autoarray::AutoArray<char> B(8*1024,false);
	libmaus2::bitio::CompactArrayWriterFile compactout(outputfilename,2 /* bits per symbol */);

	if ( ! rc )
		std::cerr << "[V] not storing reverse complements" << std::endl;

	// forward mapping table
	libmaus2::autoarray::AutoArray<uint8_t> ftable(256,false);
	// rc mapping for mapped symbols
	libmaus2::autoarray::AutoArray<uint8_t> ctable(256,false);

	std::fill(ftable.begin(),ftable.end(),4);
	std::fill(ctable.begin(),ctable.end(),4);
	ftable['a'] = ftable['A'] = 0;
	ftable['c'] = ftable['C'] = 1;
	ftable['g'] = ftable['G'] = 2;
	ftable['t'] = ftable['T'] = 3;
	uint64_t insize = 0;

	ctable[0] = 3; // A->T
	ctable[1] = 2; // C->G
	ctable[2] = 1; // G->C
	ctable[3] = 0; // T->A

	libmaus2::aio::OutputStreamInstance::unique_ptr_type metaOut(new libmaus2::aio::OutputStreamInstance(metaoutputfilename));
	libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,0);
	uint64_t nseq = 0;
	std::vector<uint64_t> lvec;

	for ( uint64_t i = 0; i < inputfilenames.size(); ++i )
	{
		std::string const fn = inputfilenames[i];
		libmaus2::aio::InputStreamInstance CIS(fn);
		libmaus2::lz::BufferedGzipStream::unique_ptr_type BGS;
		std::istream * istr = 0;
		if ( gz )
		{
			libmaus2::lz::BufferedGzipStream::unique_ptr_type tBGS(
				new libmaus2::lz::BufferedGzipStream(CIS));
			BGS = UNIQUE_PTR_MOVE(tBGS);
			istr = BGS.get();
		}
		else
		{
			istr = &CIS;
		}
		libmaus2::fastx::StreamFastAReaderWrapper fain(*istr);
		libmaus2::fastx::StreamFastAReaderWrapper::pattern_type pattern;

		while ( fain.getNextPatternUnlocked(pattern) )
		{
			if ( verbose )
				std::cerr << (i+1) << " " << stripAfterDot(basename(fn)) << " " << pattern.sid << "...";

			libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,pattern.spattern.size());
			lvec.push_back(pattern.spattern.size());
			libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,0);

			// map symbols
			for ( uint64_t j = 0; j < pattern.spattern.size(); ++j )
				pattern.spattern[j] = ftable[static_cast<uint8_t>(pattern.spattern[j])];

			// replace blocks of N symbols by random bases
			uint64_t l = 0;
			// number of replaced blocks
			uint64_t nr = 0;
			while ( l < pattern.spattern.size() )
			{
				// skip regular bases
				while ( l < pattern.spattern.size() && pattern.spattern[l] < 4 )
					++l;
				assert ( l == pattern.spattern.size() || pattern.spattern[l] == 4 );

				// go to end of non regular bases block
				uint64_t h = l;
				while ( h < pattern.spattern.size() && pattern.spattern[h] == 4 )
					++h;

				// if non regular block is not empty
				if ( h-l )
				{
					// replace by random bases
					for ( uint64_t j = l; j < h; ++j )
						pattern.spattern[j] = (libmaus2::random::Random::rand8() & 3);

					// write bounds
					libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,l);
					libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,h);
					// add to interval counter
					nr += 1;
				}

				l = h;
			}

			// make sure there are no more irregular bases
			for ( uint64_t j = 0; j < pattern.spattern.size(); ++j )
				assert ( pattern.spattern[j] < 4 );

			// go back to start of meta data
			metaOut->seekp( - static_cast<int64_t>(2*nr+1)*sizeof(uint64_t), std::ios::cur );
			// write number of intervals replaced
			libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,nr);
			// skip interval bounds already written
			metaOut->seekp(   static_cast<int64_t>(2*nr  )*sizeof(uint64_t), std::ios::cur );

			// write bases
			compactout.write(pattern.spattern.c_str(),pattern.spattern.size());

			// write reverse complement if requested
			if ( rc )
			{
				// reverse complement
				std::reverse(pattern.spattern.begin(),pattern.spattern.end());
				for ( uint64_t j = 0; j < pattern.spattern.size(); ++j )
					pattern.spattern[j] = ctable[static_cast<uint8_t>(pattern.spattern[j])];

				// write
				compactout.write(pattern.spattern.c_str(),pattern.spattern.size());
			}

			insize += pattern.spattern.size()+1;
			nseq += 1;

			if ( verbose )
				std::cerr << "done, input size " << formatBytes(pattern.spattern.size()+1) << " acc " << formatBytes(insize) << std::endl;
		}
	}

	metaOut->seekp(0);
	libmaus2::util::NumberSerialisation::serialiseNumber(*metaOut,nseq);
	metaOut->flush();
	metaOut.reset();

	libmaus2::aio::InputStreamInstance::unique_ptr_type metaISI(new libmaus2::aio::InputStreamInstance(metaoutputfilename));
	// number of sequences
	uint64_t const rnseq = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI);
	assert ( nseq == rnseq );
	for ( uint64_t i = 0; i < nseq; ++i )
	{
		// length of sequence
		uint64_t const l = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI);
		assert ( l == lvec[i] );
		uint64_t const nr = libmaus2::util::NumberSerialisation::deserialiseNumber(*metaISI);
		// skip replaced intervals
		metaISI->ignore(2*nr*sizeof(uint64_t));
	}
	assert ( metaISI->peek() == std::istream::traits_type::eof() );

	std::cerr << "Done, total input size " << insize << std::endl;

	compactout.flush();

	return EXIT_SUCCESS;
}
Esempio n. 11
0
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 )
	{
		Pindex->flush(std::string(indexfilename));
	}

	return EXIT_SUCCESS;
}