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// Copyright (c) 2020 Robert Vaser
#ifndef BIOSOUP_SEQUENCE_HPP_
#define BIOSOUP_SEQUENCE_HPP_
#include <algorithm>
#include <atomic>
#include <cctype>
#include <cstdint>
#include <string>
namespace biosoup {
struct Sequence {
public:
Sequence() = default;
Sequence(const std::string& name, const std::string& data)
: Sequence(name.c_str(), name.size(), data.c_str(), data.size()) {}
Sequence(
const char* name, std::uint32_t name_len,
const char* data, std::uint32_t data_len)
: id(num_objects++),
name(name, name_len),
data(data, data_len),
quality() {}
Sequence(
const std::string& name,
const std::string& data,
const std::string& quality)
: Sequence(
name.c_str(), name.size(),
data.c_str(), data.size(),
quality.c_str(), quality.size()) {}
Sequence(
const char* name, std::uint32_t name_len,
const char* data, std::uint32_t data_len,
const char* quality, std::uint32_t quality_len)
: id(num_objects++),
name(name, name_len),
data(data, data_len),
quality(quality, quality_len) {}
Sequence(const Sequence&) = default;
Sequence& operator=(const Sequence&) = default;
Sequence(Sequence&&) = default;
Sequence& operator=(Sequence&&) = default;
~Sequence() = default;
void ReverseAndComplement() { // (optional) Watson-Crick base pairing
for (auto& it : data) {
switch (static_cast<char>(std::toupper(static_cast<unsigned char>(it)))) {
case 'A': it = 'T'; break;
case 'C': it = 'G'; break;
case 'G': it = 'C'; break;
case 'T': case 'U': it = 'A'; break;
case 'R': it = 'Y'; break; // A || G
case 'Y': it = 'R'; break; // C || T (U)
case 'K': it = 'M'; break; // G || T (U)
case 'M': it = 'K'; break; // A || C
case 'S': break; // C || G
case 'W': break; // A || T (U)
case 'B': it = 'V'; break; // !A
case 'D': it = 'H'; break; // !C
case 'H': it = 'D'; break; // !G
case 'V': it = 'B'; break; // !T (!U)
default: break; // N || -
}
}
std::reverse(data.begin(), data.end());
std::reverse(quality.begin(), quality.end());
}
static std::atomic<std::uint32_t> num_objects;
std::uint32_t id; // (optional) initialize num_objects to 0
std::string name;
std::string data;
std::string quality; // (optional) Phred quality scores
};
} // namespace biosoup
#endif // BIOSOUP_SEQUENCE_HPP_
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