Allele.hpp

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// Copyright 2010 Complete Genomics, Inc.
//
// Licensed under the Apache License, Version 2.0 (the "License"); you
// may not use this file except in compliance with the License. You
// may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
// implied. See the License for the specific language governing
// permissions and limitations under the License.

#ifndef CGATOOLS_VARIANTS_ALLELE_HPP_
#define CGATOOLS_VARIANTS_ALLELE_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/variants/Call.hpp"

#include <string>
#include <vector>

namespace cgatools { namespace variants {

    class Locus;

    class Allele
    {
    public:
        Allele()
            : locus_(0)
        {
        }

        Allele(const Locus* locus)
            : locus_(locus)
        {
        }

        const std::vector<size_t>& getCallOffsets() const
        {
            return callOffsets_;
        }

        const Call& getCall(size_t index) const;

        std::string getAlleleSequence() const;

        std::string getRefSequence() const;

        const std::string& getHapLink() const;

        std::string getXRef() const;

        int32_t getMinVarScoreVAF() const;

        int32_t getMinVarScoreEAF() const;

        Call::VarQuality getMinVarQuality() const;

        bool hasNoCalls() const;

        void clearCalls();

        void addCallOffset(size_t offset);

        void setLocus(const Locus* locus);

    private:
        const Locus* locus_;
        std::vector<size_t> callOffsets_;
    };

} } // cgatools::variants

#endif // CGATOOLS_VARIANTS_ALLELE_HPP_

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