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//
// RapMap - Rapid and accurate mapping of short reads to transcriptomes using
// quasi-mapping.
// Copyright (C) 2015, 2016 Rob Patro, Avi Srivastava, Hirak Sarkar
//
// This file is part of RapMap.
//
// RapMap 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.
//
// RapMap 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 RapMap. If not, see <http://www.gnu.org/licenses/>.
//
#ifndef __RAP_MAP_INDEX_HPP__
#define __RAP_MAP_INDEX_HPP__
#include <fstream>
#include <memory>
//#include "jellyfish/jellyfish.hpp"
#include "jellyfish/file_header.hpp"
#include "jellyfish/binary_dumper.hpp"
#include "jellyfish/hash_counter.hpp"
#include "jellyfish/mapped_file.hpp"
#include "JFRaw.hpp"
#include "spdlog/spdlog.h"
#include <cereal/types/unordered_map.hpp>
#include <cereal/types/vector.hpp>
#include <cereal/types/string.hpp>
#include <cereal/archives/binary.hpp>
#include "RapMapUtils.hpp"
#include "ScopedTimer.hpp"
class RapMapIndex {
using PositionList = std::vector<uint32_t>;
using KmerInfoList = std::vector<rapmap::utils::KmerInfo>;
using EqClassList = std::vector<rapmap::utils::EqClass>;
//using MerMapT = jellyfish::cooperative::hash_counter<rapmap::utils::my_mer>;
using FileMerArray = jellyfish::large_hash::array_raw<rapmap::utils::my_mer>;
using EqClassLabelVec = std::vector<uint32_t>;
//using KmerIndex = std::unordered_map<uint64_t, TranscriptList, rapmap::utils::KmerKeyHasher>;
//using IntervalIndex = std::unordered_map<uint64_t, rapmap::utils::KmerInterval, rapmap::utils::KmerKeyHasher>;
public:
RapMapIndex();
bool load(std::string& indexPrefix);
KmerInfoList kmerInfos;
std::unique_ptr<char> rawHashMem{nullptr};
std::unique_ptr<FileMerArray> merHash{nullptr};
EqClassList eqClassList;
EqClassLabelVec eqLabelList;
PositionList posList;
std::vector<std::string> txpNames;
std::vector<uint32_t> txpLens;
std::vector<uint8_t> fwdJumpTable;
std::vector<uint8_t> revJumpTable;
};
#endif //__RAP_MAP_INDEX_HPP__
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