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// Author: David Alexander
#pragma once
#include <boost/range.hpp>
#include <boost/shared_array.hpp>
#include <boost/utility.hpp>
#include <string>
#include <vector>
#include <ConsensusCore/Feature.hpp>
#include <ConsensusCore/Types.hpp>
namespace ConsensusCore {
/// \brief An object containing observed features from a sequencing run.
struct SequenceFeatures
{
public:
explicit SequenceFeatures(const std::string& seq);
int Length() const { return sequence_.Length(); }
Feature<char> Sequence() const { return sequence_; }
/// Access to the sequence bases
const char& operator[](int i) const { return sequence_[i]; }
char ElementAt(int i) const { return (*this)[i]; }
private:
Feature<char> sequence_;
};
/// \brief A features object that contains PulseToBase QV metrics
struct QvSequenceFeatures : public SequenceFeatures
{
Feature<float> SequenceAsFloat;
Feature<float> InsQv;
Feature<float> SubsQv;
Feature<float> DelQv;
Feature<float> DelTag;
Feature<float> MergeQv;
explicit QvSequenceFeatures(const std::string& seq);
QvSequenceFeatures(const std::string& seq, const float* insQv, const float* subsQv,
const float* delQv, const float* delTag, const float* mergeQv);
QvSequenceFeatures(const std::string& seq, const Feature<float> insQv,
const Feature<float> subsQv, const Feature<float> delQv,
const Feature<float> delTag, const Feature<float> mergeQv);
QvSequenceFeatures(const std::string& seq, const unsigned char* insQv,
const unsigned char* subsQv, const unsigned char* delQv,
const unsigned char* delTag, const unsigned char* mergeQv);
};
/// \brief A features object that contains sequence in channel space.
struct ChannelSequenceFeatures : SequenceFeatures
{
Feature<int> Channel;
explicit ChannelSequenceFeatures(const std::string& seq);
ChannelSequenceFeatures(const std::string& seq, const std::vector<int>& channel);
};
}
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