Map2Sam.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_MAP2SAM_HPP_
#define CGA_TOOLS_COMMAND_MAP2SAM_HPP_ 1


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

namespace cgatools { namespace command {

    class Map2SamConfig {
    public:
        Map2SamConfig() 
            :recordsFrom_(0)
            ,recordsTo_(std::numeric_limits<size_t>::max())
            ,skipNotMapped_(false)
            ,addMateSequenceAndScore_(false)
            ,mateSvCandidates_(false)
        {}

        size_t recordsFrom_;
        size_t recordsTo_;
        bool   skipNotMapped_;
        bool   addMateSequenceAndScore_;
        bool   mateSvCandidates_;

        util::RangeSet::StringVector exportRegions_;

        std::string inputReadsFileName_;
        std::string inputMappingsFileName_;
        std::string inputLibFileName_;
        std::string referenceFileName_;
        std::string outputFileName_;
        
        std::string commandLine_;
    };

    class Map2Sam : public Command
    {
    public:
        Map2Sam(const std::string& name);

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

    private:
        Map2SamConfig config_;
    };

} } // cgatools::command

#endif // CGA_TOOLS_COMMAND_MAP2SAM_HPP_

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