Evidence2Sam.hpp

Go to the documentation of this file.

// 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"

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::RangeSet::StringVector exportRegions_;

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

        std::string commandLine_;
    };

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

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

    private:
        Evidence2SamConfig config_;
    };
    
    class Cigar {
        friend std::ostream& operator<< (std::ostream& out, const Cigar& cigar);
    public:
        class CigarElement {
        public:
            CigarElement(char type, size_t length)
                : type_(type), length_(length) {}
            int getSequenceLength() const;
            char    type_;
            size_t  length_;
        };
        typedef std::vector<CigarElement> ParsedCigar;

        Cigar() {}

        Cigar(const std::string &cigar, bool mergeNeighbours = false, bool removeZeros = false) 
        {
            parse(cigar,mergeNeighbours,removeZeros);
        }

        void parse(const std::string &cigar, bool mergeNeighbours, bool removeZeros);

        size_t getSequenceLength() const;
        size_t getReferenceLength() const;
        
        const ParsedCigar& getParsedCigar() const {return parsedCigar_;}

        void push_back(const CigarElement &e) {parsedCigar_.push_back(e);}
        void add_back(const CigarElement &e);

        CigarElement &operator[](size_t i) {return parsedCigar_[i];}
        CigarElement &back() {return parsedCigar_.back();}

        size_t size() const {return parsedCigar_.size();}
        //removes paddings in the beginning and at the end of the CIGAR to satisfy SAMValidate from Pickard
        void trancatePaddings();
    protected:
        ParsedCigar parsedCigar_;
    };

    class SamSequenceSplitter {
    public:
        SamSequenceSplitter(const Cigar& extCigar, const std::string& dnbSequence, 
            const std::string& dnbScore, bool negativeStrand);

        Cigar               srcExtCigar_;
        std::string         srcSequence_;
        std::string         srcScores_;

        Cigar               cigar_;
        std::stringstream   sequence_;
        std::stringstream   scores_;

        Cigar               tagCigar_;
        std::stringstream   tagSequence_;
        std::stringstream   tagScores_;
    protected:
        void convert();
    };

} } // cgatools::command

#endif // CGA_TOOLS_COMMAND_EVIDENCE2SAM_HPP_

---