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th: 1736
/*!
* @file sequence.hpp
*
* @brief Sequence class header file
*/
#pragma once
#include
#include
#include
#include
namespace bioparser {
template
class FastaParser;
template
class FastqParser;
}
namespace racon {
class Sequence;
std::unique_ptr createSequence(const std::string& name,
const std::string& data);
class Sequence {
public:
~Sequence() = default;
const std::string& name() const {
return name_;
}
const std::string& data() const {
return data_;
}
const std::string& reverse_complement() const {
return reverse_complement_;
}
const std::string& quality() const {
return quality_;
}
const std::string& reverse_quality() const {
return reverse_quality_;
}
void create_reverse_complement();
void transmute(bool has_name, bool has_data, bool has_reverse_data);
friend bioparser::FastaParser;
friend bioparser::FastqParser;
friend std::unique_ptr createSequence(const std::string& name,
const std::string& data);
private:
Sequence(const char* name, uint32_t name_length, const char* data,
uint32_t data_length);
Sequence(const char* name, uint32_t name_length, const char* data,
uint32_t data_length, const char* quality, uint32_t quality_length);
Sequence(const std::string& name, const std::string& data);
Sequence(const Sequence&) = delete;
const Sequence& operator=(const Sequence&) = delete;
std::string name_;
std::string data_;
std::string reverse_complement_;
std::string quality_;
std::string reverse_quality_;
};
}
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