SamRecord.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_SAM_RECORD_HPP_
#define CGA_TOOLS_SAM_RECORD_HPP_ 1


#include "cgatools/core.hpp"

#include <vector>
#include <string>

namespace cgatools { namespace reference {
    class CrrFile;
}}

namespace cgatools { namespace mapping {

    typedef std::pair<uint16_t,uint16_t> UInt16Pair;

    class SamRecord
    {
        friend std::ostream& operator<< (std::ostream& ost, const SamRecord& r);
    public:
        enum RecordType
        {
            DEFAULT = 0,
            BASE_MAPPING,
            EVIDENCE,
            EVIDENCE_CACHE
        };

        typedef std::vector<SamRecord *> SamRecords;

        SamRecord(
            const std::string& readName, bool isMapped, bool onNegativeStrand, bool isPrimary,
            uint8_t side, uint16_t chr, uint32_t position,
            const std::string& extCigar,
            uint8_t mappingQuality,
            const std::string& fullReadSequence,
            const std::string& fullReadScores,
            UInt16Pair sequenceStartAndLength
            );

        virtual ~SamRecord() {}

        bool correctPosition(const reference::CrrFile& reference);

        RecordType  typeId_;

        std::string readName_;
        bool        isMapped_;
        bool        onNegativeStrand_;
        bool        isPrimary_;
        bool        isGroupPrimary_;
        uint8_t     side_;
        uint16_t    chr_;
        uint32_t    position_;
        std::string extCigar_;
        uint8_t     mappingQuality_;

        std::string fullReadSequence_;
        std::string fullReadScores_;
        bool        isSvCandidate_;

        // start and length of the sequence corresponding to this mapping(0) or the mate (1)
        UInt16Pair sequenceStartAndLength_[2];

        SamRecords  mates_;

        virtual bool isConsistent() const;
    protected:
    };
    
    class SamFileHeaderBlock
    {
        friend std::ostream& operator<< (std::ostream& ostr,const SamFileHeaderBlock& block);
    public:
        typedef std::vector<SamFileHeaderBlock> Children;

        SamFileHeaderBlock(std::string id = "None")
            :id_(id),type_(id),separator_("\t")
        {}
        SamFileHeaderBlock(const std::string &id, 
            const std::string& type, const std::string& separator, const std::string& value)
            :id_(id),type_(type),separator_(separator),value_(value)
        {}
        SamFileHeaderBlock(
            const std::string &id, const std::string& separator, const std::string& value)
            :id_(id),type_(id),separator_(separator),value_(value)
        {}

        const SamFileHeaderBlock& getChild(const std::string &child) const;

        bool operator== (const SamFileHeaderBlock& other) const {
            return id_ == other.id_;
        }

        SamFileHeaderBlock& get(const SamFileHeaderBlock& b);
        SamFileHeaderBlock& add(const SamFileHeaderBlock& b);

        std::string id_;
        std::string type_;
        std::string separator_;
        std::string value_;
        Children children_;
    };

    class EvidenceSamRecord;
    class SamSequenceSplitter;

    class SamRecordGenerator
    {
    public:
        static const char SAM_SEPARATOR = '\t';

        SamRecordGenerator(
            std::ostream& outSamFile, 
            const reference::CrrFile& reference,
            bool mateSvCandidates, 
            bool addMateSequenceAndScore,
            bool addMateSequenceAndScoreIfMateUnmapped,
            bool printAlleleInfo
            )
        :   
            outSamFile_(outSamFile), reference_(reference),
            mateSvCandidates_(mateSvCandidates),
            addMateSequenceAndScore_(addMateSequenceAndScore),
            addMateSequenceAndScoreIfMateUnmapped_(addMateSequenceAndScoreIfMateUnmapped),
            printAlleleInfo_(printAlleleInfo)
        {}

        void mappingRecordToSam(const SamRecord& record);

        void setHeader(const SamFileHeaderBlock& header);
    protected:

        void printMateSequence(const std::string &mateSeq, const std::string &mateScore);

        void printReadGroup();
        void printNegativeGapTag(const mapping::SamSequenceSplitter &splitter);
    
        void flagAsSVCandidate();
        void printAlleleInfoTag(const mapping::EvidenceSamRecord& evidenceRecord);

        uint32_t adjustedPosition(const SamRecord& record ) const;

        std::ostream &  outSamFile_;
        const reference::CrrFile& reference_;
        bool                mateSvCandidates_;
        bool                addMateSequenceAndScore_;
        bool                addMateSequenceAndScoreIfMateUnmapped_;
        bool                printAlleleInfo_;
        SamFileHeaderBlock  header_;
        std::string         readGroup_;

    };

    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;
            bool operator== (const CigarElement& e) const {return type_==e.type_ && length_==e.length_;}

            char    type_;
            size_t  length_;
        };
        typedef std::vector<CigarElement> ParsedCigar;

        Cigar(bool mergeNeighbours = false, bool removeZeros = false) 
            :mergeNeighbours_(mergeNeighbours), removeZeros_(removeZeros)
        {}

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

        void parse(const std::string &cigar);

        size_t getSequenceLength() const;
        size_t getReferenceLength() const;

        const ParsedCigar& getParsedCigar() const {return parsedCigar_;}

        void add(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();

        Cigar pack() const;

        bool operator== (const Cigar& c) const {return parsedCigar_==c.parsedCigar_;}
    protected:
        void push_back(const CigarElement &e) {parsedCigar_.push_back(e);}
        void add_back(const CigarElement &e);

        bool mergeNeighbours_;
        bool removeZeros_;
        ParsedCigar parsedCigar_;
    };

} } // cgatools::mapping

#endif // CGA_TOOLS_SAM_RECORD_HPP_

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