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/**
>HEADER
Copyright (c) 2013 Rob Patro robp@cs.cmu.edu
This file is part of Sailfish.
Sailfish 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.
Sailfish 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 Sailfish. If not, see <http://www.gnu.org/licenses/>.
<HEADER
**/
#ifndef __MULTITHREADED_BAM_PARSER__
#define __MULTITHREADED_BAM_PARSER__
#include <cstdio>
#include <cstdlib>
#include <vector>
#include <thread>
#include <atomic>
#include <iostream>
#include "api/BamReader.h"
#include "api/BamAlignment.h"
#include <boost/filesystem.hpp>
#include <boost/range/irange.hpp>
#include "tbb/concurrent_queue.h"
namespace bfs = boost::filesystem;
struct ReadSeq {
char* seq = nullptr;
size_t len = 0;
char* name = nullptr;
size_t nlen = 0;
};
class MultithreadedBAMParser {
public:
MultithreadedBAMParser( std::vector<bfs::path>& files );
~MultithreadedBAMParser();
bool start();
bool nextAlignment(BamTools::BamAlignment*& seq);
void finishedWithAlignment(BamTools::BamAlignment*& s);
private:
std::vector<bfs::path>& inputStreams_;
bool parsing_;
std::thread* parsingThread_;
tbb::concurrent_bounded_queue<BamTools::BamAlignment*> alnQueue_, seqContainerQueue_;
BamTools::BamAlignment* alnStructs_;
const size_t queueCapacity_ = 5000000;
};
//#include "Parser.cpp"
#endif // __MULTITHREADED_BAM_PARSER__
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