Call.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_CALL_HPP_
#define CGATOOLS_VARIANTS_CALL_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/reference/CrrFile.hpp"
#include "cgatools/util/DelimitedFile.hpp"
#include <string>

namespace cgatools { namespace variants {

    struct Call
    {
    public:
        class VarQualityField : public util::DelimitedFieldParser
        {
        public:
            VarQualityField(const std::string& name, std::vector<std::string>* varFilter);

            void parse(const char* first, const char* last);

        private:
            std::vector<std::string>* varFilter_;
        };

        class VarFilterField : public util::DelimitedFieldParser
        {
        public:
            VarFilterField(const std::string& name, std::vector<std::string>* varFilter);

            void parse(const char* first, const char* last);

        private:
            std::vector<std::string>* varFilter_;
        };

        class TotalScoreField : public util::DelimitedFieldParser
        {
        public:
            TotalScoreField(
                const std::string& name,
                int32_t* varScoreVAF,
                int32_t* varScoreEAF);

            void parse(const char* first, const char* last);

        private:
            int32_t* varScoreVAF_;
            int32_t* varScoreEAF_;
        };

        struct AlternativeCall
        {
            AlternativeCall()
                : score_(0)
            {
            }

            AlternativeCall(const std::string& alleleSeq, int32_t score)
                : alleleSeq_(alleleSeq),
                  score_(score)
            {
            }

            std::string alleleSeq_;
            int32_t     score_;
        };

        class AlternativeCallsField : public util::DelimitedFieldParser
        {
        public:
            AlternativeCallsField(
                const std::string& name,
                std::vector<AlternativeCall>* alternativeCalls);

            void parse(const char* first, const char* last);

        private:
            std::vector<AlternativeCall>* alternativeCalls_;
        };

        static const uint16_t ALL_HAPLOTYPES;

        static const uint16_t UNKNOWN_PLOIDY;

        static const int32_t EMPTY_SCORE;

        Call ();

        std::string calledSequence(const reference::CrrFile& crr) const;

        std::string refSequence(const reference::CrrFile& crr) const;

        bool isRefConsistent(const reference::CrrFile& crr) const;

        bool hasNoCalls() const;

        void addFieldParsers(util::DelimitedFile& df, const reference::CrrFile& crr);

        void addVarFilter(const std::string& filter);

        std::ostream& write(std::ostream& out,
                            const reference::CrrFile& crr,
                            const char sep = '\t') const;

        static void parseAlternativeCalls(
            const char* first, const char* last, std::vector<AlternativeCall>& alternativeCalls);

        static void parseVarFilter(
            const char* first, const char* last, std::vector<std::string>& varFilter);

        static std::string getHeader (const char separator = '\t');

        uint32_t locus_;

        uint16_t ploidy_;

        uint16_t haplotype_;

        reference::Range range_;

        std::string varType_;

        std::string reference_;

        std::string alleleSeq_;

        int32_t varScoreVAF_;

        int32_t varScoreEAF_;

        std::vector<std::string> varFilter_;

        std::string hapLink_;

        std::string xRef_;

        std::string alleleFreq_;

        std::vector<AlternativeCall> alternativeCalls_;
    };

    void upgradeOldFieldValues(Call& c);

} } // cgatools::variants

#endif // CGATOOLS_VARIANTS_CALL_HPP_

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