/**
    bambam
    Copyright (C) 2009-2017 German Tischler
    Copyright (C) 2011-2013 Genome Research Limited

    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 "config.h"

#include <iostream>
#include <queue>

#include <libmaus2/aio/OutputStreamInstance.hpp>

#include <libmaus2/bambam/BamAlignment.hpp>
#include <libmaus2/bambam/BamBlockWriterBaseFactory.hpp>
#include <libmaus2/bambam/BamMultiAlignmentDecoderFactory.hpp>
#include <libmaus2/bambam/BamWriter.hpp>
#include <libmaus2/bambam/ProgramHeaderLineSet.hpp>

#include <libmaus2/util/ArgInfo.hpp>
#include <libmaus2/util/GetObject.hpp>
#include <libmaus2/util/PutObject.hpp>
#include <libmaus2/util/TempFileRemovalContainer.hpp>

#include <biobambam2/Licensing.hpp>

static int getDefaultLevel() {return libmaus2::lz::DeflateDefaults::getDefaultLevel();}
static int getDefaultVerbose() { return 1; }

#include <libmaus2/lz/BgzfDeflateOutputCallbackMD5.hpp>
#include <libmaus2/bambam/BgzfDeflateOutputCallbackBamIndex.hpp>
static int getDefaultMD5() { return 0; }
static int getDefaultIndex() { return 0; }

int bamfilterrg(::libmaus2::util::ArgInfo const & arginfo)
{
	::libmaus2::util::TempFileRemovalContainer::setup();

	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::BamAlignmentDecoderWrapper::unique_ptr_type decwrapper(
		libmaus2::bambam::BamMultiAlignmentDecoderFactory::construct(
			arginfo
		)
	);
	libmaus2::bambam::BamAlignmentDecoder & dec = decwrapper->getDecoder();
	::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,
		"bamfilterrg", // ID
		"bamfilterrg", // 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 ( libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo) != std::string() )
			md5filename = libmaus2::bambam::BamBlockWriterBaseFactory::getMD5FileName(arginfo);
		else
			std::cerr << "[V] no filename for md5 given, not creating hash" << std::endl;

		if ( md5filename.size() )
		{
			::libmaus2::lz::BgzfDeflateOutputCallbackMD5::unique_ptr_type Tmd5cb(new ::libmaus2::lz::BgzfDeflateOutputCallbackMD5);
			Pmd5cb = std::move(Tmd5cb);
			cbs.push_back(Pmd5cb.get());
		}
	}
	libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Pindex;
	if ( arginfo.getValue<unsigned int>("index",getDefaultIndex()) )
	{
		if ( libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo) != std::string() )
			indexfilename = libmaus2::bambam::BamBlockWriterBaseFactory::getIndexFileName(arginfo);
		else
			std::cerr << "[V] no filename for index given, not creating index" << std::endl;

		if ( indexfilename.size() )
		{
			libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex::unique_ptr_type Tindex(new libmaus2::bambam::BgzfDeflateOutputCallbackBamIndex(tmpfileindex));
			Pindex = std::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));

	bool haverefidlist = false;
	uint64_t const nref = header.getNumRef();
	libmaus2::bitio::BitVector BV(nref);
	for ( uint64_t i = 0; i < nref; ++i )
		BV.erase(i);

	if ( arginfo.hasArg("refids") )
	{
		std::vector<std::string> vreadgroups;
		for ( uint64_t i = 0; i < nref; ++i )
			vreadgroups.push_back(header.getRefIDName(i));
		::libmaus2::trie::Trie<char> trienofailure;
		trienofailure.insertContainer(vreadgroups);
		::libmaus2::trie::LinearHashTrie<char,uint32_t>::unique_ptr_type LHTnofailure(trienofailure.toLinearHashTrie<uint32_t>());

		libmaus2::aio::InputStreamInstance ISI(arginfo.getUnparsedValue("refids",std::string()));
		while ( ISI )
		{
			std::string line;
			std::getline(ISI,line);
			if ( line.size() )
			{
				int64_t const id = LHTnofailure->searchCompleteNoFailureZ(line.c_str());
				if ( id >= 0 )
				{
					std::cerr << "[V] keeping " << line << " id " << id << std::endl;
					BV.set(id);
				}
				else
				{
					std::cerr << "[W] ref id " << line << " not found in header" << std::endl;
				}
			}
		}
		haverefidlist = true;
	}

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

	if ( ! haverefidlist )
		while ( dec.readAlignment() )
		{
			algn.serialise(writer->getStream());
			if ( verbose && (++c & (1024*1024-1)) == 0 )
				std::cerr << "[V] " << c/(1024*1024) << std::endl;
		}
	else
		while ( dec.readAlignment() )
		{
			int64_t const refid = algn.getRefID();
			if ( refid >= 0 && BV.get(refid) )
				algn.serialise(writer->getStream());
			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;
}

int main(int argc, char * argv[])
{
	try
	{
		::libmaus2::util::ArgInfo const arginfo(argc,argv);

		for ( uint64_t i = 0; i < arginfo.restargs.size(); ++i )
			if (
				arginfo.restargs[i] == "-v"
				||
				arginfo.restargs[i] == "--version"
			)
			{
				std::cerr << ::biobambam2::Licensing::license();
				return EXIT_SUCCESS;
			}
			else if (
				arginfo.restargs[i] == "-h"
				||
				arginfo.restargs[i] == "--help"
			)
			{
				std::cerr << ::biobambam2::Licensing::license();
				std::cerr << std::endl;
				std::cerr << "Key=Value pairs:" << std::endl;
				std::cerr << std::endl;

				std::vector< std::pair<std::string,std::string> > V;

				V.push_back ( std::pair<std::string,std::string> ( "level=<["+::biobambam2::Licensing::formatNumber(getDefaultLevel())+"]>", libmaus2::bambam::BamBlockWriterBaseFactory::getBamOutputLevelHelpText() ) );
				V.push_back ( std::pair<std::string,std::string> ( "verbose=<["+::biobambam2::Licensing::formatNumber(getDefaultVerbose())+"]>", "print progress information" ) );
				V.push_back ( std::pair<std::string,std::string> ( "refids=<[]>", "file containing ref ids to be kept (default: keep all)" ) );
				V.push_back ( std::pair<std::string,std::string> ( "md5=<["+::biobambam2::Licensing::formatNumber(getDefaultMD5())+"]>", "create md5 check sum (default: 0)" ) );
				V.push_back ( std::pair<std::string,std::string> ( "md5filename=<filename>", "file name for md5 check sum (default: extend output file name)" ) );
				V.push_back ( std::pair<std::string,std::string> ( "index=<["+::biobambam2::Licensing::formatNumber(getDefaultIndex())+"]>", "create BAM index (default: 0)" ) );
				V.push_back ( std::pair<std::string,std::string> ( "indexfilename=<filename>", "file name for BAM index file (default: extend output file name)" ) );
				V.push_back ( std::pair<std::string,std::string> ( "tmpfile=<filename>", "prefix for temporary files, default: create files in current directory" ) );

				::biobambam2::Licensing::printMap(std::cerr,V);

				std::cerr << std::endl;

				return EXIT_SUCCESS;
			}

		return bamfilterrg(arginfo);
	}
	catch(std::exception const & ex)
	{
		std::cerr << ex.what() << std::endl;
		return EXIT_FAILURE;
	}
}
