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// Copyright (c) 2011-2013, Pacific Biosciences of California, Inc.
//
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted (subject to the limitations in the
// disclaimer below) provided that the following conditions are met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
//
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
//
// * Neither the name of Pacific Biosciences nor the names of its
// contributors may be used to endorse or promote products derived
// from this software without specific prior written permission.
//
// NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
// GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
// BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED
// WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES
// OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
// DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF
// USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
// ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
// OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
// OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
// SUCH DAMAGE.
// Author: Patrick Marks, David Alexander
#pragma once
#include <string>
#include <vector>
#include "Types.hpp"
namespace ConsensusCore
{
enum MutationType
{
INSERTION, DELETION, SUBSTITUTION
};
/// \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);
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.
/// In the case of an insertion, Start=End= template position before the new bases are 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;
};
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);
}
#include "Mutation-inl.hpp"
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