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#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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