PhasedAllele.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_PHASEDALLELE_HPP_
#define CGATOOLS_VARIANTS_PHASEDALLELE_HPP_ 1


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

namespace cgatools { namespace variants {

    class PhasedAllele
    {
    public:
        PhasedAllele()
            : pos_(1, 0)
        {
        }

        void addCall(const Call& call, const Locus& locus, const reference::CrrFile& crr);

        void addSequence(const Call& call, const Locus& locus, const std::string& sequence);

        bool hasHapLink(const std::string& hapLink) const;

        const std::string& allele() const
        {
            return allele_;
        }

        const std::vector<uint32_t>& pos() const
        {
            return pos_;
        }

        const std::vector<const Call*>& calls() const
        {
            return calls_;
        }

        const std::vector<const Locus*>& loci() const
        {
            return loci_;
        }

    private:
        std::string allele_;
        std::vector<uint32_t> pos_; 
        std::vector<const Call*> calls_;
        std::vector<const Locus*> loci_;
    };

} } // cgatools::variants

#endif // CGATOOLS_VARIANTS_PHASEDALLELE_HPP_

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