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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 __RAPMAP_SA_INDEX_HPP__
#define __RAPMAP_SA_INDEX_HPP__
#include <cereal/types/unordered_map.hpp>
#include <cereal/types/vector.hpp>
#include <cereal/types/string.hpp>
#include <cereal/archives/binary.hpp>
#include "spdlog/spdlog.h"
#include "spdlog/fmt/ostr.h"
#include "spdlog/fmt/fmt.h"
#include "bit_array.h"
//#include "bitmap.h"
//#include "shared.h"
#include "rank9b.h"
#include <cstdio>
#include <vector>
#include <memory>
#include <fstream>
#include "RapMapUtils.hpp"
template <typename IndexT, typename HashT>
class RapMapSAIndex {
public:
using IndexType = IndexT;
using HashType = HashT;
struct BitArrayDeleter {
void operator()(BIT_ARRAY* b) {
if(b != nullptr) {
bit_array_free(b);
}
}
};
using BitArrayPointer = std::unique_ptr<BIT_ARRAY, BitArrayDeleter>;
RapMapSAIndex();
// Given a position, p, in the concatenated text,
// return the corresponding transcript
IndexT transcriptAtPosition(IndexT p);
bool isDecoy(IndexT p);
uint64_t getNumDecoys();
bool load(const std::string& indDir);
std::vector<IndexT> SA;
BitArrayPointer bitArray{nullptr};
uint64_t numDecoys{0};
uint64_t firstDecoyIndex{std::numeric_limits<uint64_t>::max()};
//BitArrayPointer decoyArray{nullptr};
std::unique_ptr<rank9b> rankDict{nullptr};
std::string seq;
std::vector<std::string> txpNames;
std::vector<IndexT> txpOffsets;
std::vector<IndexT> txpLens;
std::vector<IndexT> positionIDs;
std::vector<uint32_t> txpCompleteLens;
std::vector<rapmap::utils::SAIntervalWithKey<IndexT>> kintervals;
HashT khash;
};
#endif //__RAPMAP_SA_INDEX_HPP__
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