/*
    libmaus2
    Copyright (C) 2016 German Tischler

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
#include <libmaus2/suffixsort/bwtb3m/BwtComputeSSA.hpp>

template<typename a_type, typename b_type>
struct PairFirstProjectorType
{
	static a_type project(std::pair<a_type,b_type> const & P)
	{
		return P.first;
	}
};

template<typename a_type, typename b_type>
struct PairSecondProjectorType
{
	static a_type project(std::pair<a_type,b_type> const & P)
	{
		return P.second;
	}
};

struct QueueElement
{
	uint64_t r;
	uint64_t p;
	uint64_t id;

	QueueElement(uint64_t const rr = 0, uint64_t const rp = 0, uint64_t const rid = 0)
	: r(rr), p(rp), id(rid)
	{

	}

	bool operator<(QueueElement const & O) const
	{
		if ( r != O.r )
			return r > O.r;
		else if ( p != O.p )
			return p > O.p;
		else
			return id > O.id;
	}
};

// load histogram map
static std::vector<uint64_t> loadHMap(std::string const & hist)
{
	libmaus2::aio::InputStreamInstance::unique_ptr_type Phist(new libmaus2::aio::InputStreamInstance(hist));
	// deserialise number map
	std::map<int64_t,uint64_t> const hmap = ::libmaus2::util::NumberMapSerialisation::deserialiseMap<std::istream,int64_t,uint64_t>(*Phist);
	// number vector
	std::vector<uint64_t> D;

	if ( hmap.size() && hmap.begin()->first >= 0 )
	{
		// top symbol
		int64_t const topsym = hmap.rbegin()->first;
		// space for top symbol + 1 after
		D.resize(topsym+2);
		// copy frequences
		for ( std::map<int64_t,uint64_t>::const_iterator ita = hmap.begin(); ita != hmap.end(); ++ita )
		{
			D [ ita->first ] = ita->second;
			// std::cerr << "[HIN]\t" << ita->first << "\t" << ita->second << std::endl;
		}
		// erase last value in D
		D [ D.size()-1 ] = 0;

		// compute prefix sums
		uint64_t s = 0;
		for ( uint64_t i = 0; i < D.size(); ++i )
		{
			uint64_t const t = D[i];
			D[i] = s;
			s += t;
		}

		#if 0
		for ( uint64_t i = 0; i < D.size(); ++i )
			std::cerr << "[HIST]\t" << i << "\t" << D[i] << std::endl;
		#endif
	}

	return D;
}

static uint64_t computeNF(std::vector<uint64_t> const & H, std::vector<uint64_t> const & NZH, uint64_t const bm, std::vector<uint64_t> * HID = 0)
{
	uint64_t nf = 0;
	uint64_t s = 0;
	for ( uint64_t i = 0; i < NZH.size(); ++i )
	{
		if ( s && s >= bm )
		{
			s = 0;
			nf += 1;
		}

		uint64_t const sym = NZH[i];
		uint64_t const occ = H[sym+1]-H[sym];

		s += occ;

		// std::cerr << "sym=" << sym << " occ=" << occ << " s=" << s << std::endl;

		if ( HID )
			HID->push_back(nf);
	}

	if ( s )
	{
		s = 0;
		nf += 1;
	}

	return nf;
}

static uint64_t computeSplit(uint64_t const tnumfiles, std::vector<uint64_t> const & H, std::vector<uint64_t> const & NZH, uint64_t const n)
{
	// look for smallest split value s.t. number of files is <= tnumfiles
	uint64_t bl = 0, bh = n;
	while ( bh - bl > 2 )
	{
		uint64_t const bm = (bh + bl)>>1;
		uint64_t const nf = computeNF(H,NZH,bm);

		// std::cerr << "bl=" << bl << ",bh=" << bh << ",bm=" << bm << " nf=" << nf << std::endl;

		// number of files too large? bm is not a valid solution
		if ( nf > tnumfiles )
			bl = bm+1;
		// number of files small enough, bm is a valid solution
		else
			bh = bm+1;
	}

	uint64_t split = bl;
	for ( uint64_t i = bl; i < bh; ++i )
		if ( computeNF(H,NZH,i) <= tnumfiles )
		{
			split = i;
			break;
		}
	// std::cerr << "bl=" << bl << ",bh=" << bh << " split=" << split << " numfiles=" << computeNF(H,NZH,split) << std::endl;

	return split;
}

struct PreIsaInput
{
	typedef PreIsaInput this_type;
	typedef std::unique_ptr<this_type> unique_ptr_type;

	libmaus2::aio::ConcatInputStream CIS;
	libmaus2::aio::SynchronousGenericInput<uint64_t> SGI;

	PreIsaInput(std::vector<std::string> const & fn, uint64_t const roffset = 0)
	: CIS(fn), SGI(CIS,64*1024)
	{
		if ( roffset )
		{
			CIS.clear();
			CIS.seekg(roffset * 2 * sizeof(uint64_t));
		}
	}

	bool getNext(std::pair<uint64_t,uint64_t> & P)
	{
		bool const ok = SGI.getNext(P.first);

		if ( ok )
		{
			#if !defined(NDEBUG)
			bool const ok2 =
			#endif
				SGI.getNext(P.second);
			#if !defined(NDEBUG)
			assert ( ok2 );
			#endif
		}

		return ok;
	}
};

struct PreIsaAccessor
{
	typedef PreIsaAccessor this_type;

	mutable libmaus2::aio::ConcatInputStream CIS;
	// number of samples in file
	uint64_t n;

	typedef libmaus2::util::ConstIterator< this_type,std::pair<uint64_t,uint64_t> > iterator;

	PreIsaAccessor(std::vector<std::string> const & fn) : CIS(fn)
	{
		CIS.clear();
		CIS.seekg(0,std::ios::end);
		assert ( CIS.tellg() % (2*sizeof(uint64_t)) == 0 );
		n = CIS.tellg() / (2*sizeof(uint64_t));
		CIS.clear();
		CIS.seekg(0,std::ios::beg);
		// std::cerr << "constructed " << this << std::endl;
	}
	~PreIsaAccessor()
	{
		//std::cerr << "[V] destructing " << this << std::endl;
	}

	std::pair<uint64_t,uint64_t> get(uint64_t const i) const
	{
		//std::cerr << this << " " << "get(" << i << ")" << " n=" << n << std::endl;
		CIS.clear();
		CIS.seekg(i*2*sizeof(uint64_t));
		// std::cerr << CIS.tellg() << " " << i*2*sizeof(uint64_t) << std::endl;
		assert ( static_cast<std::streampos>(CIS.tellg()) == static_cast<std::streampos>(i*2*sizeof(uint64_t)) );
		uint64_t p0, p1;
		CIS.read(reinterpret_cast<char *>(&p0), sizeof(uint64_t));
		CIS.read(reinterpret_cast<char *>(&p1), sizeof(uint64_t));
		return std::pair<uint64_t,uint64_t>(p0,p1);
	}

	std::pair<uint64_t,uint64_t> operator[](uint64_t const i) const
	{
		return get(i);
	}

	iterator begin()
	{
		iterator it(this,0);
		return it;
	}

	iterator end()
	{
		iterator it(this,n);
		return it;
	}

	struct PFComp
	{
		bool operator()(std::pair<uint64_t,uint64_t> const & A, std::pair<uint64_t,uint64_t> const & B) const
		{
			return A.first < B.first;
		}
	};


	static std::vector< std::pair<uint64_t,uint64_t > > getOffsets(std::vector<std::string> const & fn, std::vector< uint64_t > const & splitblocks)
	{
		this_type acc(fn);

		assert ( splitblocks.size() );
		uint64_t const num = splitblocks.size()-1;

		std::vector< std::pair<uint64_t,uint64_t > >V(num+1);
		V[num] = std::pair<uint64_t,uint64_t >(splitblocks.back(), acc.n);

		for ( uint64_t i = 0; i < num; ++i )
		{
			uint64_t const rr = splitblocks[i];
			iterator it = std::lower_bound(acc.begin(),acc.end(),std::pair<uint64_t,uint64_t>(rr,0),PFComp());
			assert ( it == acc.end() || it[0].first >= rr );
			assert ( it == acc.begin() || it[-1].first < rr );
			V[i] = std::pair<uint64_t,uint64_t > (rr,it-acc.begin());
		}

		return V;
	}
};

struct IsaTriple
{
	uint64_t s;
	uint64_t r;
	uint64_t p;

	IsaTriple() : s(0), r(0), p(0) {}
	IsaTriple(uint64_t const & rs, uint64_t const & rr, uint64_t const & rp)
	: s(rs), r(rr), p(rp) {}

	bool operator<(IsaTriple const & rhs) const
	{
		if ( s != rhs.s )
			return s < rhs.s;
		else if ( r != rhs.r )
			return r < rhs.r;
		else
			return p < rhs.p;
	}

	bool operator==(IsaTriple const & rhs) const
	{
		return
			s == rhs.s
			&&
			r == rhs.r
			&&
			p == rhs.p;
	}

	bool operator!=(IsaTriple const & rhs) const
	{
		return !(*this == rhs);
	}
};

void libmaus2::suffixsort::bwtb3m::BwtComputeSSA::computeSSA(
	std::string bwt,
	uint64_t const sasamplingrate,
	uint64_t const isasamplingrate,
	std::string const tmpfilenamebase,
	bool const copyinputtomemory,
	uint64_t const numthreads,
	uint64_t const maxsortmem,
	uint64_t const maxtmpfiles,
	std::ostream * logstr,
	std::string const ref_isa_fn,
	std::string const ref_sa_fn
)
{
	// original bwt name
	std::string const origbwt = bwt;
	// dictionary prefix
	std::string const dictprefix = libmaus2::util::OutputFileNameTools::clipOff(origbwt,".bwt");
	// character histogram
	std::string const histfn = dictprefix + ".hist";
	// pre isa
	std::string const preisa = dictprefix + ".preisa";
	// meta (sampling rate) for pre isa
	std::string const preisameta = preisa + ".meta";

	uint64_t preisasamplingrate;
	{
		libmaus2::aio::InputStreamInstance ISI(preisameta);
		preisasamplingrate = libmaus2::util::NumberSerialisation::deserialiseNumber(ISI);
	}


	if ( copyinputtomemory )
	{
		std::string const nbwt = "mem://copied_" + bwt;
		libmaus2::aio::InputStreamInstance ininst(bwt);
		libmaus2::aio::OutputStreamInstance outinst(nbwt);
		uint64_t const fs = libmaus2::util::GetFileSize::getFileSize(ininst);
		libmaus2::util::GetFileSize::copy(ininst,outinst,fs);
		if ( logstr )
			*logstr << "[V] copied " << bwt << " to " << nbwt << std::endl;
		bwt = nbwt;
	}

	// load ref_isa if we have any
	libmaus2::autoarray::AutoArray<uint64_t>::unique_ptr_type ref_isa;
	if ( ref_isa_fn.size() )
	{
		libmaus2::aio::InputStreamInstance I(ref_isa_fn);
		uint64_t ref_isa_samplingrate;
		libmaus2::serialize::Serialize<uint64_t>::deserialize(I,&ref_isa_samplingrate);
		assert ( ref_isa_samplingrate == isasamplingrate );
		libmaus2::autoarray::AutoArray<uint64_t>::unique_ptr_type Tptr(new libmaus2::autoarray::AutoArray<uint64_t>(I));
		ref_isa = std::move(Tptr);
	}
	// load ref_sa if we have any
	libmaus2::autoarray::AutoArray<uint64_t>::unique_ptr_type ref_sa;
	if ( ref_sa_fn.size() )
	{
		libmaus2::aio::InputStreamInstance I(ref_sa_fn);
		uint64_t ref_sa_samplingrate;
		libmaus2::serialize::Serialize<uint64_t>::deserialize(I,&ref_sa_samplingrate);
		assert ( ref_sa_samplingrate == sasamplingrate );
		libmaus2::autoarray::AutoArray<uint64_t>::unique_ptr_type Tptr(new libmaus2::autoarray::AutoArray<uint64_t>(I));
		ref_sa = std::move(Tptr);
	}

	// temp file for sa
	std::string const satmpfn = tmpfilenamebase + "_sa_tmp";
	libmaus2::util::TempFileRemovalContainer::addTempFile(satmpfn);
	// temp file for isa
	std::string const isatmpfn = tmpfilenamebase + "_isa_tmp";
	libmaus2::util::TempFileRemovalContainer::addTempFile(isatmpfn);

	// check sa sampling rate
	if ( libmaus2::rank::PopCnt8<sizeof(unsigned long)>::popcnt8(sasamplingrate) != 1 )
	{
		libmaus2::exception::LibMausException lme;
		lme.getStream() << "sasamplingrate is not a power of 2" << std::endl;
		lme.finish();
		throw lme;
	}
	// check isa sampling rate
	if ( libmaus2::rank::PopCnt8<sizeof(unsigned long)>::popcnt8(isasamplingrate) != 1 )
	{
		libmaus2::exception::LibMausException lme;
		lme.getStream() << "isasamplingrate is not a power of 2" << std::endl;
		lme.finish();
		throw lme;
	}

	// bit masks for sa and isa sampling rates
	uint64_t const sasamplingmask = sasamplingrate-1;
	uint64_t const isasamplingmask = isasamplingrate-1;

	// input file vector
	std::vector<std::string> Vbwtin(1,bwt);
	// length of input file in symbols
	uint64_t const n = libmaus2::huffman::RLDecoder::getLength(Vbwtin,numthreads);

	// load character histogram and compute prefix sums
	std::vector<uint64_t> const H = loadHMap(histfn);

	uint64_t numnonzeroocc = 0;
	// sequence of non zero occ symbols
	std::vector<uint64_t> NZH;
	for ( uint64_t i = 1; i < H.size(); ++i )
		// if non zero occ count for symbol i-1
		if ( H[i] != H[i-1] )
		{
			numnonzeroocc++;
			// non zero occ symbol vector
			NZH.push_back(i-1);
		}

	// number of symbols with non zero occurence count
	if ( logstr )
		*logstr << "[D] numnonzeroocc=" << numnonzeroocc << std::endl;

	// target number of files
	uint64_t const tnumfiles = 256;
	// compute split
	uint64_t const split = computeSplit(tnumfiles, H, NZH, n);
	if ( logstr )
		*logstr << "[D] split=" << split << std::endl;

	// vector symbol to file for symbols in NZH
	std::vector<uint64_t> HID;
	computeNF(H, NZH, split, &HID);

	// map symbol -> file
	std::vector<int64_t> filemap;
	if ( NZH.size() )
		filemap.resize(NZH.back()+1);
	// initialise all to -1
	std::fill(filemap.begin(),filemap.end(),-1);

	// number of files used
	int64_t const numfiles = HID.size() ? static_cast<int64_t>(HID.back()+1) : 0;
	// bit vector marking files used by more than 1 symbol
	std::vector<bool> filemulti(numfiles);
	std::fill(filemulti.begin(),filemulti.end(),false);

	// compute filemulti
	uint64_t hid_low = 0;
	while ( hid_low < HID.size() )
	{
		uint64_t hid_high = hid_low+1;
		while ( hid_high < HID.size() && HID[hid_high] == HID[hid_low] )
			++hid_high;

		if ( hid_high-hid_low > 1 )
			for ( uint64_t i = hid_low; i < hid_high; ++i )
				filemulti.at(HID[i]) = true;

		hid_low = hid_high;
	}

	for ( uint64_t i = 0; i < HID.size(); ++i )
	{
		int64_t const sym = NZH[i];
		uint64_t const mapping = HID[i];

		filemap .at ( sym ) = mapping;
		if ( logstr )
			*logstr << sym << "\t" << mapping << "\t" << filemulti[filemap[sym]] << "\t" << filemap[sym] << "\t" << H[sym] << std::endl;
	}

	if ( logstr )
		*logstr << "[V] numfiles=" << numfiles << std::endl;

	std::vector<std::string> isain(1,preisa);
	bool deletein = false;

	// maximum symbol
	int64_t const maxsym = static_cast<int64_t>(H.size())-1;

	std::vector< std::vector<uint64_t> > Vblocksymhist;
	// block rank start vector
	std::vector< uint64_t > Vsplitblocks;

	if ( 1 /* maxsym > 256 */ )
	{
		// compute accumulated block sym freq counts
		std::string const rlhisttmp = tmpfilenamebase + "_rlhist_tmp";
		std::string const blockhisttmp = tmpfilenamebase + "_rlhist_final";
		libmaus2::util::TempFileRemovalContainer::addTempFile(blockhisttmp);
		libmaus2::huffman::RLDecoder::getFragmentSymHistograms(bwt,blockhisttmp,rlhisttmp,0,maxsym,numthreads /* numpacks */,numthreads);

		// block sym freq count
		std::vector<uint64_t> rlblockhist(maxsym+1,0);
		// accumulated block sym freq count
		std::vector<uint64_t> rlblockhistacc(maxsym+1,0);
		libmaus2::aio::InputStreamInstance::unique_ptr_type rlhistISI(new libmaus2::aio::InputStreamInstance(blockhisttmp));

		// decode block of 0 values
		for ( uint64_t i = 0; i < rlblockhist.size(); ++i )
			rlblockhist[i] = libmaus2::util::NumberSerialisation::deserialiseNumber(*rlhistISI) - rlblockhistacc[i];

		Vsplitblocks.push_back(std::accumulate(rlblockhistacc.begin(),rlblockhistacc.end(),0ull));
		assert ( Vsplitblocks.at(0) == 0ull );

		// decode rest of blocks
		while ( rlhistISI->peek() != std::istream::traits_type::eof() )
		{
			for ( uint64_t i = 0; i < rlblockhist.size(); ++i )
				rlblockhist[i] = libmaus2::util::NumberSerialisation::deserialiseNumber(*rlhistISI) - rlblockhistacc[i];

			std::vector<uint64_t> bhist(maxsym+1,0);
			for ( uint64_t i = 0; i < rlblockhistacc.size(); ++i )
				bhist[i] = H[i] + rlblockhistacc[i];
			Vblocksymhist.push_back(bhist);

			for ( uint64_t i = 0; i < rlblockhist.size(); ++i )
				rlblockhistacc[i] += rlblockhist[i];

			Vsplitblocks.push_back(std::accumulate(rlblockhistacc.begin(),rlblockhistacc.end(),0ull));
		}

		#if 0
		std::vector<uint64_t> bhist(maxsym+1,0);
		for ( uint64_t i = 0; i < rlblockhistacc.size(); ++i )
			bhist[i] = H[i] + rlblockhistacc[i];
		Vblocksymhist.push_back(bhist);
		#endif

		assert ( Vsplitblocks.back() == n );

		libmaus2::aio::FileRemoval::removeFile(blockhisttmp);
	}
	else
	{
		std::string const rlhisttmp = tmpfilenamebase + "_rlhist_tmp";
		std::string const blockhisttmp = tmpfilenamebase + "_rlhist_final";
		libmaus2::util::TempFileRemovalContainer::addTempFile(blockhisttmp);
		libmaus2::huffman::RLDecoder::getBlockSymHistograms(bwt,blockhisttmp,rlhisttmp,0,maxsym,numthreads);

		libmaus2::aio::InputStreamInstance::unique_ptr_type rlhistISI(new libmaus2::aio::InputStreamInstance(blockhisttmp));
		// rlhistISI->seekg(0,std::ios::end);
		// std::cerr << rlhistISI->tellg() << std::endl;
		// rlhistISI->clear();
		// rlhistISI->seekg(0,std::ios::beg);

		uint64_t const tpacks = numthreads;
		uint64_t const packsize = (n + tpacks-1)/tpacks;

		std::vector<uint64_t> rlblockhistacc(maxsym+1,0);
		std::vector<uint64_t> rlblockhistprev(maxsym+1,0);
		std::vector<uint64_t> rlblockhist(maxsym+1,0);
		uint64_t ac = 0;
		uint64_t bc = 0;
		uint64_t maxbs = 0;
		std::vector<uint64_t> Vbs;
		while ( rlhistISI->peek() != std::istream::traits_type::eof() )
		{
			// compute block size
			uint64_t bs = 0;
			for ( uint64_t i = 0; i < rlblockhist.size(); ++i )
			{
				rlblockhist[i] = libmaus2::util::NumberSerialisation::deserialiseNumber((*rlhistISI));
				bs += (rlblockhist[i]-rlblockhistprev[i]);
			}
			maxbs = std::max(bs,maxbs);

			if ( ac > packsize )
			{
				assert ( std::accumulate(rlblockhistacc.begin(),rlblockhistacc.end(),0ull) == ac );

				Vbs.push_back(ac);
				Vblocksymhist.push_back(rlblockhistacc);
				// std::cerr << "bc=" << bc << std::endl;

				ac = 0;
				bc = 0;
				std::fill(rlblockhistacc.begin(),rlblockhistacc.end(),0ull);
			}

			for ( uint64_t i = 0; i < rlblockhist.size(); ++i )
			{
				rlblockhistacc[i] += rlblockhist[i]-rlblockhistprev[i];
				rlblockhistprev[i] = rlblockhist[i];
			}
			ac += bs;
			bc += 1;
		}

		assert ( std::accumulate(rlblockhistacc.begin(),rlblockhistacc.end(),0ull) == ac );

		if ( ac )
		{
			Vbs.push_back(ac);
			Vblocksymhist.push_back(rlblockhistacc);
			std::fill(rlblockhistacc.begin(),rlblockhistacc.end(),0ull);
		}

		Vblocksymhist.push_back(rlblockhistacc);

		#if 0
		std::cerr << "rlblockhist.size()=" << rlblockhist.size() << " " << Vbs.size() << " " << packsize << " maxbs=" << maxbs << std::endl;
		for ( uint64_t i = 0; i < Vblocksymhist.size(); ++i )
		{
			std::cerr << std::accumulate(Vblocksymhist[i].begin(),Vblocksymhist[i].end(),0ull) << std::endl;
		}

		exit(0);
		#endif

		Vsplitblocks = std::vector< uint64_t >(Vbs.size()+1);
		uint64_t as = 0;
		for ( uint64_t i = 0; i < Vsplitblocks.size(); ++i )
		{
			Vsplitblocks[i] = as;
			as += Vbs[i];
		}
		Vsplitblocks[Vbs.size()] = as;

		// iterate over symbols
		for ( uint64_t i = 0; i < rlblockhistacc.size(); ++i )
		{
			uint64_t c = H[i];

			// iterate over blocks
			for ( uint64_t j = 0; j < Vblocksymhist.size(); ++j )
			{
				uint64_t const t = Vblocksymhist[j][i];
				Vblocksymhist[j][i] = c;
				c += t;
			}
		}

		#if 0
		assert (
			std::accumulate(
				Vblocksymhist.back().begin(),
				Vblocksymhist.back().end(),
				0ull
			) == n
		);
		#endif

		libmaus2::aio::FileRemoval::removeFile(blockhisttmp);
	}

	libmaus2::parallel::StdSpinLock salock;
	libmaus2::parallel::StdSpinLock isalock;

	// number of run length blocks
	uint64_t const numrblocks =  Vsplitblocks.size() - 1;
	std::vector<std::string> Vsatmpfn(numrblocks);
	std::vector<std::string> Visatmpfn(numrblocks);
	libmaus2::autoarray::AutoArray< libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >::unique_ptr_type  > Asaout(numrblocks);
	libmaus2::autoarray::AutoArray< libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >::unique_ptr_type  > Aisaout(numrblocks);

	for ( uint64_t i = 0; i < numrblocks; ++i )
	{
		Vsatmpfn[i] = satmpfn + "_" + libmaus2::util::NumberSerialisation::formatNumber(i,6);
		libmaus2::util::TempFileRemovalContainer::addTempFile(Vsatmpfn[i]);
		libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >::unique_ptr_type Tptr(new libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >(Vsatmpfn[i],8*1024));
		Asaout[i] = std::move(Tptr);
	}
	for ( uint64_t i = 0; i < numrblocks; ++i )
	{
		Visatmpfn[i] = isatmpfn + "_" + libmaus2::util::NumberSerialisation::formatNumber(i,6);
		libmaus2::util::TempFileRemovalContainer::addTempFile(Visatmpfn[i]);
		libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >::unique_ptr_type Tptr(new libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> >(Visatmpfn[i],8*1024));
		Aisaout[i] = std::move(Tptr);
	}

	// iterate pre isa sampling rate times (pre isa samples are at most at distance preisasamplingrate from each other)
	for ( uint64_t run = 0; run < preisasamplingrate; ++run )
	{
		if ( logstr )
			*logstr << "[V] entering run " << (run+1) << "/" << preisasamplingrate << std::endl;

		// check input order
		{
			PreIsaInput PII(isain,0);
			std::pair<uint64_t,uint64_t> P, Pprev;
			bool haveprev = false;
			while ( PII.getNext(P) )
			{
				if ( haveprev )
				{
					bool ok = ( P.first >= Pprev.first );
					ok = ok && ( P.first != Pprev.first || P.second == Pprev.second );
					if ( ! ok )
					{
						std::cerr << "failed order " << Pprev.first << " " << P.first << std::endl;
					}
					assert ( ok );
				}
				Pprev = P;
				haveprev = true;
			}
		}

		std::vector< std::pair<uint64_t,uint64_t > > const piasplit = PreIsaAccessor::getOffsets(isain,Vsplitblocks);
		assert ( piasplit.size() == Vsplitblocks.size() );

		#if 0
		for ( uint64_t i = 0; i < piasplit.size(); ++i )
		{
			PreIsaAccessor PIA(isain);
			std::cerr << "[PIA] " << i << " " << piasplit[i].first << " " << piasplit[i].second << " " << PIA[piasplit[i].second].first << std::endl;
			assert ( i == 0 || PIA[piasplit[i].second-1].first < piasplit[i].first );
		}
		#endif

		std::vector<std::string> goutfilenames((piasplit.size()-1)*numfiles);
		libmaus2::parallel::StdSpinLock goutfilenameslock;

		libmaus2::exception::LibMausException::unique_ptr_type lmex;
		libmaus2::parallel::StdSpinLock lmexlock;

		#if defined(_OPENMP)
		#pragma omp parallel for num_threads(numthreads)
		#endif
		for ( uint64_t t = 1; t < piasplit.size(); ++t )
		{
			try
			{
				uint64_t const rfrom = piasplit[t-1].first;
				uint64_t const rto = piasplit[t].first;
				uint64_t const preisafrom = piasplit[t-1].second;

				libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> > & saout = *(Asaout[t-1]);
				libmaus2::aio::SynchronousGenericOutput<std::pair<uint64_t,uint64_t> > & isaout = *(Aisaout[t-1]);

				{
				libmaus2::parallel::StdSpinLock::scope_lock_type slock(salock);
				if ( logstr )
					*logstr << "[V] t=" << t << " rfrom=" << rfrom << " rto=" << rto << " preisafrom=" << preisafrom << std::endl;
				}

				std::ostringstream threadtmpprefixstr;
				threadtmpprefixstr << tmpfilenamebase << "_" << run << "_" << (t-1);
				std::string const threadtmpprefix = threadtmpprefixstr.str();

				// output file pointers
				libmaus2::autoarray::AutoArray<libmaus2::aio::OutputStreamInstance::unique_ptr_type > Aout(numfiles);
				// output file buffers
				libmaus2::autoarray::AutoArray<libmaus2::aio::SynchronousGenericOutput<uint64_t>::unique_ptr_type > Sout(numfiles);
				// sorting output buffers (for files storing data for more than one symbol)
				libmaus2::autoarray::AutoArray<libmaus2::sorting::SortingBufferedOutputFile<IsaTriple>::unique_ptr_type > Tout(numfiles);
				// output file names
				std::vector<std::string> outfilenames(numfiles);
				// multi sort output file names
				std::vector<std::string> multisortfilenames(numfiles);

				//std::cerr << "[V+] " << numfiles << std::endl;

				// iterate over output files for this run
				for ( int64_t i = 0; i < numfiles; ++i )
				{
					std::ostringstream fnostr;
					fnostr << threadtmpprefix << "_" << std::setw(6) << std::setfill('0') << i << std::setw(0);
					std::string const fn = fnostr.str();
					outfilenames[i] = fn;

					libmaus2::util::TempFileRemovalContainer::addTempFile(fn);
					libmaus2::aio::OutputStreamInstance::unique_ptr_type Tptr(new libmaus2::aio::OutputStreamInstance(fn));
					Aout[i] = std::move(Tptr);

					libmaus2::aio::SynchronousGenericOutput<uint64_t>::unique_ptr_type Sptr(new libmaus2::aio::SynchronousGenericOutput<uint64_t>(*(Aout[i]),64*1024));
					Sout[i] = std::move(Sptr);

					multisortfilenames[i] = fn + ".multisort";
					if ( filemulti[i] )
					{
						libmaus2::util::TempFileRemovalContainer::addTempFile(multisortfilenames[i]);
						libmaus2::sorting::SortingBufferedOutputFile<IsaTriple>::unique_ptr_type Tptr(
							new libmaus2::sorting::SortingBufferedOutputFile<IsaTriple>(multisortfilenames[i],64*1024)
						);
						Tout[i] = std::move(Tptr);
					}
				}

				{
					libmaus2::parallel::StdSpinLock::scope_lock_type slock(goutfilenameslock);

					for ( int64_t i = 0; i < numfiles; ++i )
					{
						goutfilenames . at( i * (piasplit.size()-1) + (t-1) ) = outfilenames[i];
					}

				}

				// open decoder for RL
				libmaus2::huffman::RLDecoder rldec(std::vector<std::string>(1,bwt),rfrom,1 /* numthreads */);

				std::vector<uint64_t> HH = Vblocksymhist[t-1];

				PreIsaInput PII(isain,preisafrom);

				std::pair<uint64_t,uint64_t> P;
				#if 0
				uint64_t lc = rfrom;
				#endif
				uint64_t c = rfrom;

				std::pair<int64_t,uint64_t> currun(-1,0);

				while ( PII.getNext(P) && (P.first < rto) )
				{
					bool const ok = P.first >= rfrom;

					if ( ! ok )
					{
						std::cerr << "P.first=" << P.first << " rfrom=" << rfrom << std::endl;
					}

					assert ( P.first >= rfrom );

					if ( (P.first & sasamplingmask) == 0 )
					{
						saout.put(std::pair<uint64_t,uint64_t>(P.first,P.second));

						if ( ref_sa )
						{
							bool const ok = (*ref_sa)[P.first / sasamplingrate] == P.second;
							if ( ! ok )
							{
								std::cerr << "P.first=" << P.first << std::endl;
								std::cerr << "P.first/sasamplingrate=" << P.first/sasamplingrate << std::endl;
								std::cerr << "P.second=" << P.second << std::endl;
								std::cerr << "expected=" << (*ref_sa)[P.first / sasamplingrate] << std::endl;
							}
							assert ( ok );
							//std::cerr << "ok 1" << std::endl;
						}
					}
					if ( (P.second & isasamplingmask) == 0 )
					{
						isaout.put(std::pair<uint64_t,uint64_t>(P.second,P.first));

						if ( ref_isa )
						{
							assert ( (*ref_isa)[P.second / isasamplingrate] == P.first );
							//std::cerr << "ok 2" << std::endl;
						}
					}

					#if 0
					if ( (c >> 26) != (lc >> 26) )
					{
						std::cerr << "run=" << (run+1) << "/" << preisasamplingrate << " frac=" << static_cast<double>(c) / n << std::endl;
						lc = c;
					}
					#endif

					while ( c < P.first )
					{
						// no more symbols in run? load next one
						if ( ! currun.second )
							currun = rldec.decodeRun();

						int64_t const sym = currun.first;
						assert ( sym >= 0 );
						assert ( sym < static_cast<int64_t>(HH.size()) );
						assert ( currun.second );

						uint64_t const dif = P.first - c;
						uint64_t const touse = std::min(dif,currun.second);

						HH[sym] += touse;
						c += touse;
						currun.second -= touse;
					}

					if ( ! currun.second )
						currun = rldec.decodeRun();

					int64_t const sym = currun.first;
					assert ( sym >= 0 );
					assert ( sym < static_cast<int64_t>(HH.size()) );
					assert ( currun.second );

					uint64_t const rout = HH[sym];
					uint64_t const pout = (P.second + n - 1)%n;
					assert ( filemap[sym] >= 0 );
					uint64_t const fileid = filemap[sym];

					// std::cerr << "sym=" << sym << " fileid=" << fileid << std::endl;

					bool const multi = filemulti[fileid];

					if ( multi )
					{
						Tout[fileid]->put(IsaTriple(sym,rout,pout));
					}
					else
					{
						Sout[fileid]->put(rout);
						Sout[fileid]->put(pout);
					}
				}

				// post sort files storing data for more than one symbol
				for ( int64_t fileid = 0; fileid < numfiles; ++fileid )
					if ( filemulti[fileid] )
					{
						libmaus2::sorting::SortingBufferedOutputFile<IsaTriple>::merger_ptr_type merger(Tout[fileid]->getMerger());
						IsaTriple T;
						IsaTriple Tprev;
						bool haveprev = false;

						while ( merger->getNext(T) )
						{
							if ( haveprev )
								assert ( T.r >= Tprev.r );

							Sout[fileid]->put(T.r);
							Sout[fileid]->put(T.p);

							Tprev = T;
							haveprev = true;
						}
					}

				for ( int64_t i = 0; i < numfiles; ++i )
				{
					Sout[i]->flush();
					Sout[i].reset();
					Aout[i]->flush();
					Aout[i].reset();
				}

				for ( int64_t i = 0; i < numfiles; ++i )
					libmaus2::aio::FileRemoval::removeFile(multisortfilenames[i]);
			}
			catch(libmaus2::exception::LibMausException const & ex)
			{
				libmaus2::parallel::ScopeStdSpinLock slock(lmexlock);
				if ( ! lmex )
				{
					libmaus2::exception::LibMausException::unique_ptr_type tptr(ex.uclone());
					lmex = std::move(tptr);
				}
			}
			catch(std::exception const & ex)
			{
				libmaus2::parallel::ScopeStdSpinLock slock(lmexlock);
				if ( ! lmex )
				{
					libmaus2::exception::LibMausException::unique_ptr_type tptr(libmaus2::exception::LibMausException::uclone(ex));
					lmex = std::move(tptr);
				}
			}
		}

		if ( lmex )
			throw *lmex;

		for ( int64_t fileid = 0; fileid < numfiles; ++fileid )
			if ( filemulti[fileid] )
			{

				std::priority_queue<QueueElement> Q;
				libmaus2::autoarray::AutoArray<PreIsaInput::unique_ptr_type> Ain(piasplit.size()-1);
				for ( uint64_t t = 1; t < piasplit.size(); ++t )
				{
					uint64_t const id = t-1;

					PreIsaInput::unique_ptr_type Tptr(new PreIsaInput(std::vector<std::string>(1,goutfilenames . at( fileid * (piasplit.size()-1) + (id) ))));
					Ain.at(id) = std::move(Tptr);

					std::pair<uint64_t,uint64_t> P;
					if ( Ain[id]->getNext(P) )
						Q.push(QueueElement(P.first,P.second,id));
				}

				std::ostringstream tmpfnstr;
				tmpfnstr << tmpfilenamebase << "_" << run << "_merge_" << fileid;
				std::string const tmpfn = tmpfnstr.str();
				libmaus2::util::TempFileRemovalContainer::addTempFile(tmpfn);
				libmaus2::aio::OutputStreamInstance::unique_ptr_type out(new libmaus2::aio::OutputStreamInstance(tmpfn));
				libmaus2::aio::SynchronousGenericOutput<uint64_t>::unique_ptr_type sout(new libmaus2::aio::SynchronousGenericOutput<uint64_t>(*out,8*1024));
				std::pair<uint64_t,uint64_t> Pprev;
				bool haveprev = false;
				while ( Q.size() )
				{
					QueueElement const E = Q.top();
					Q.pop();

					if ( haveprev )
					{
						assert ( E.r >= Pprev.first );
						assert ( E.r != Pprev.first || E.p == Pprev.second );
					}

					sout->put(E.r);
					sout->put(E.p);

					std::pair<uint64_t,uint64_t> P;
					if ( Ain.at(E.id)->getNext(P) )
						Q.push(QueueElement(P.first,P.second,E.id));

					Pprev.first = E.r;
					Pprev.second = E.p;
					haveprev = true;
				}
				sout->flush();
				sout.reset();
				out.reset();

				{
				PreIsaInput PII(std::vector<std::string>(1,tmpfn));
				std::pair<uint64_t,uint64_t> P, Pprev;
				bool haveprev = false;
				while ( PII.getNext(P) )
				{
					if ( haveprev )
					{
						assert ( P.first >= Pprev.first );
						assert ( P.first > Pprev.first || P.second == Pprev.second );
					}
					haveprev = true;
					Pprev = P;
				}
				}

				for ( uint64_t t = 1; t < piasplit.size(); ++t )
				{
					uint64_t const id = t-1;
					std::string & fn = goutfilenames . at( fileid * (piasplit.size()-1) + (id) );
					if ( id )
					{
						libmaus2::aio::OutputStreamInstance tout(fn);
					}
					else
					{
						libmaus2::aio::FileRemoval::removeFile(fn);
						fn = tmpfn;
					}
				}
			}

		if ( deletein )
			for ( uint64_t i = 0; i < isain.size(); ++i )
				libmaus2::aio::FileRemoval::removeFile(isain[i]);

		isain = goutfilenames;
		deletein = true;
	}

	for ( uint64_t i = 0; i < Asaout.size(); ++i )
	{
		Asaout[i]->flush();
		Asaout[i].reset();
	}

	for ( uint64_t i = 0; i < Aisaout.size(); ++i )
	{
		Aisaout[i]->flush();
		Aisaout[i].reset();
	}

	if ( deletein )
		for ( uint64_t i = 0; i < isain.size(); ++i )
			libmaus2::aio::FileRemoval::removeFile(isain[i]);

	libmaus2::aio::OutputStreamInstance::unique_ptr_type saout(new libmaus2::aio::OutputStreamInstance(libmaus2::util::OutputFileNameTools::clipOff(origbwt,".bwt") + ".sa"));
	::libmaus2::serialize::Serialize<uint64_t>::serialize(*saout,sasamplingrate);
	::libmaus2::serialize::Serialize<uint64_t>::serialize(*saout,(n+sasamplingrate-1)/sasamplingrate);
	libmaus2::sorting::SemiExternalKeyTupleSort::sort< std::pair<uint64_t,uint64_t>,PairFirstProjectorType<uint64_t,uint64_t>,uint64_t,PairSecondProjectorType<uint64_t,uint64_t> >(Vsatmpfn,tmpfilenamebase + "_final_sa_tmp_",*saout,n,numthreads,maxtmpfiles /* max files */,maxsortmem /* max mem */, true /* remove input */);
	saout->flush();
	saout.reset();

	for ( uint64_t i = 0; i < Vsatmpfn.size(); ++i )
		libmaus2::aio::FileRemoval::removeFile(Vsatmpfn[i]);

	libmaus2::aio::OutputStreamInstance::unique_ptr_type isaout(new libmaus2::aio::OutputStreamInstance(libmaus2::util::OutputFileNameTools::clipOff(origbwt,".bwt") + ".isa"));
	::libmaus2::serialize::Serialize<uint64_t>::serialize(*isaout,isasamplingrate);
	::libmaus2::serialize::Serialize<uint64_t>::serialize(*isaout,(n+isasamplingrate-1)/isasamplingrate);
	libmaus2::sorting::SemiExternalKeyTupleSort::sort< std::pair<uint64_t,uint64_t>,PairFirstProjectorType<uint64_t,uint64_t>,uint64_t,PairSecondProjectorType<uint64_t,uint64_t> >(Visatmpfn,tmpfilenamebase + "_final_isa_tmp_",*isaout,n,numthreads,maxtmpfiles /* max files */,maxsortmem /* max mem */, true /* remove input */);
	isaout->flush();
	isaout.reset();

	for ( uint64_t i = 0; i < Visatmpfn.size(); ++i )
		libmaus2::aio::FileRemoval::removeFile(Visatmpfn[i]);
}
