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/*!
* @file sequence.cpp
*
* @brief Sequence class source file
*/
#include <ctype.h>
#include "sequence.hpp"
namespace racon {
std::unique_ptr<Sequence> createSequence(const std::string& name,
const std::string& data) {
return std::unique_ptr<Sequence>(new Sequence(name, data));
}
Sequence::Sequence(const char* name, uint32_t name_length, const char* data,
uint32_t data_length)
: name_(name, name_length), data_(), reverse_complement_(), quality_(),
reverse_quality_() {
data_.reserve(data_length);
for (uint32_t i = 0; i < data_length; ++i) {
data_ += toupper(data[i]);
}
}
Sequence::Sequence(const char* name, uint32_t name_length, const char* data,
uint32_t data_length, const char* quality, uint32_t quality_length)
: Sequence(name, name_length, data, data_length) {
uint32_t quality_sum = 0;
for (uint32_t i = 0; i < quality_length; ++i) {
quality_sum += quality[i] - '!';
}
if (quality_sum > 0) {
quality_.assign(quality, quality_length);
}
}
Sequence::Sequence(const std::string& name, const std::string& data)
: name_(name), data_(data), reverse_complement_(), quality_(),
reverse_quality_() {
}
void Sequence::create_reverse_complement() {
if (!reverse_complement_.empty()) {
return;
}
reverse_complement_.clear();
reverse_complement_.reserve(data_.size());
for (int32_t i = data_.size() - 1; i >= 0; --i) {
switch (data_[i]) {
case 'A':
reverse_complement_ += 'T';
break;
case 'T':
reverse_complement_ += 'A';
break;
case 'C':
reverse_complement_ += 'G';
break;
case 'G':
reverse_complement_ += 'C';
break;
default:
reverse_complement_ += data_[i];
break;
}
}
reverse_quality_.clear();
reverse_quality_.reserve(quality_.size());
for (int32_t i = quality_.size() - 1; i >= 0; --i) {
reverse_quality_ += quality_[i];
}
}
void Sequence::transmute(bool has_name, bool has_data, bool has_reverse_data) {
if (!has_name) {
std::string().swap(name_);
}
if (has_reverse_data) {
create_reverse_complement();
}
if (!has_data) {
std::string().swap(data_);
std::string().swap(quality_);
}
}
}
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