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// Author: Patrick Marks, David Alexander
#pragma once
#include <ostream>
#include <string>
#include <utility>
#include <vector>
#include <ConsensusCore/Types.hpp>
#include <ConsensusCore/Utils.hpp>
namespace ConsensusCore {
enum MutationType
{
INSERTION = 0,
DELETION = 1,
SUBSTITUTION = 2
};
/// \brief Single mutation to a template sequence.
class Mutation
{
private:
MutationType type_;
int start_;
int end_;
std::string newBases_;
bool CheckInvariants() const;
public:
Mutation(MutationType type, int start, int end, std::string newBases);
Mutation(MutationType type, int position, char base);
Mutation(const Mutation& other);
// Note: this defines a default mutation. This is really only needed to fix
// SWIG compilation.
Mutation();
MutationType Type() const;
bool IsSubstitution() const;
bool IsInsertion() const;
bool IsDeletion() const;
/// \brief Template positions of the mutation.
/// Convention: the bases of the template changed by the mutation are
/// [ Start, End ).
/// For a substitution, tpl[Start..End) are mutated;
/// for a deletion, tpl[Start..End) are removed;
/// for an insertion, Start=End=template position after the
/// new bases are to be inserted.
int Start() const;
int End() const;
std::string NewBases() const;
int LengthDiff() const;
std::string ToString() const;
public:
bool operator==(const Mutation& other) const;
bool operator<(const Mutation& other) const;
public:
ScoredMutation WithScore(float score) const;
};
std::ostream& operator<<(std::ostream& out, const Mutation& m);
std::string ApplyMutation(const Mutation& mut, const std::string& tpl);
std::string ApplyMutations(const std::vector<Mutation>& muts, const std::string& tpl);
std::string MutationsToTranscript(const std::vector<Mutation>& muts, const std::string& tpl);
std::vector<int> TargetToQueryPositions(const std::vector<Mutation>& mutations,
const std::string& tpl);
class ScoredMutation : public Mutation
{
private:
float score_;
public:
ScoredMutation();
ScoredMutation(const Mutation& m, float score);
float Score() const;
std::string ToString() const;
};
std::ostream& operator<<(std::ostream& out, const ScoredMutation& m);
}
#include <ConsensusCore/Mutation-inl.hpp>
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