Evidence2Sam.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 CGA_TOOLS_COMMAND_EVIDENCE2SAM_HPP_
#define CGA_TOOLS_COMMAND_EVIDENCE2SAM_HPP_ 1


#include "cgatools/core.hpp"
#include "cgatools/command/Command.hpp"
#include "cgatools/util/RangeSet.hpp"
#include "cgatools/mapping/SamRecord.hpp"

namespace cgatools { namespace command {

    class Evidence2SamConfig {
    public:
        Evidence2SamConfig() 
            :keepDuplicates_(false)
            //,addMateSequenceAndScore_(false)
            //,addAlleleId_(false)
            ,verboseOutput_(false)
        {}

        bool   keepDuplicates_;
        //bool   addMateSequenceAndScore_;
        //bool   addAlleleId_;
        bool   verboseOutput_;

        util::StringVector exportRegions_;

        std::string evidenceDnbsFileName_;
        std::string inputLibFileName_;
        std::string referenceFileName_;
        std::string outputFileName_;

        std::string commandLine_;

        mapping::SamGeneratorConfig samGeneratorConfig_;
    };

    class Evidence2Sam : public Command
    {
    public:
        Evidence2Sam(const std::string& name);

    protected:
        int run(po::variables_map& vm);

    private:
        Evidence2SamConfig config_;
    };

} } // cgatools::command

#endif // CGA_TOOLS_COMMAND_EVIDENCE2SAM_HPP_

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