VcfRecordSource.hpp

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// Copyright 2011 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 CGA_TOOLS_CONV_VCFRECORDSOURCE_HPP_
#define CGA_TOOLS_CONV_VCFRECORDSOURCE_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/reference/CrrFile.hpp"

#include <iostream>

namespace cgatools { namespace conv {

    class VcfRecordWriter
    {
    public:
        void writeRecord(
            std::ostream& out,
            const cgatools::reference::CrrFile& crr,
            size_t sampleCount) const;

        virtual cgatools::reference::Location getLocation() const = 0;

        virtual void writeId(std::ostream& out) const
        {
            out << ".";
        }

        virtual void writeRef(std::ostream& out) const = 0;

        virtual void writeAlt(std::ostream& out) const = 0;

        virtual void writeQual(std::ostream& out) const
        {
            out << ".";
        }

        virtual void writeFilter(std::ostream& out) const
        {
            out << ".";
        }

        virtual void writeInfo(std::ostream& out) const = 0;

        virtual void writeFormat(std::ostream& out) const = 0;

        virtual void writeSample(std::ostream& out, size_t idxGenome) const = 0;

        static std::string getVcfChromosomeName(
            size_t chromosomeId,
            const cgatools::reference::CrrFile& crr);
    };

    struct VcfSubFieldHeaderRecord
    {
        enum Key
        {
            VCF_ALT    = 0,
            VCF_FILTER = 1,
            VCF_INFO   = 2,
            VCF_FORMAT = 3,
            VCF_END    = 4
        };

        VcfSubFieldHeaderRecord(
            Key key,
            const std::string& id,
            const std::string& number,
            const std::string& type,
            const std::string& description)
            : key_(key),
              id_(id),
              number_(number),
              type_(type),
              description_(description)
        {
        };

        Key         key_;
        std::string id_;
        std::string number_;
        std::string type_;
        std::string description_;
    };

    struct VcfKvHeaderRecord
    {
        VcfKvHeaderRecord(const std::string& key,
                          const std::string& value)
            : key_(key),
              value_(value)
        {
        }

        std::string key_;
        std::string value_;
    };

    class VcfRecordSource
    {
    public:
        virtual std::vector<VcfSubFieldHeaderRecord> getSubFieldHeaderRecords() const = 0;

        virtual std::string getSource(size_t idxGenome) const = 0;

        virtual std::vector<VcfKvHeaderRecord> getKeyValueHeaderRecords(size_t idxGenome) const = 0;

        virtual std::string getAssemblyId(size_t idxGenome) const = 0;


        virtual bool eof() const = 0;
        virtual VcfRecordSource& operator++() = 0;
        virtual const VcfRecordWriter& operator*() const = 0;
        virtual const VcfRecordWriter* operator->() const = 0;
    };

} } // cgatools::conv

#endif // CGA_TOOLS_CONV_VCFRECORDSOURCE_HPP_

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