#ifndef _BLASR_SAM_ALIGNMENT_HPP_
#define _BLASR_SAM_ALIGNMENT_HPP_

#include <sstream>
#include <string>

#include <pbdata/sam/CigarString.h>
#include <pbdata/sam/SAMKeywordValuePair.hpp>

class SAMAlignment
{
public:
    enum SAMAlignmentRequiredFields
    {
        S_QNAME,
        S_FLAG,
        S_RNAME,
        S_POS,
        S_MAPQV,
        S_CIGAR,
        S_RNEXT,
        S_PNEXT,
        S_TLEN,
        S_SEQ,
        S_QUAL
    };

    static const char* SAMAlignmentRequiredFieldNames[];

    std::string qName;
    unsigned int flag;
    std::string rName;
    unsigned int pos;
    short mapQV;
    CigarString cigar;
    std::string rNext;
    int pNext;
    int tLen;
    std::string seq;
    std::string qual;

    // Optional tags defined in blasr:
    // "RG" read group Id
    // "AS" alignment score
    // "XS" read alignment start position without counting previous soft clips (1 based)
    // "XE" read alignment end position without counting previous soft clips (1 based)
    // "XL" aligned read length
    // "XQ" query read length
    // "XT" # of continues reads, always 1 for blasr
    // "NM" # of subreads
    // "FI" read alignment start position (1 based)
    //
    float score;
    int xs, xe;
    int xl;
    int xq;

    std::string rg;
    int as;
    int xt;
    int nm;
    int fi;
    std::string optTagStr;
    //
    // Quality values.
    //
    std::string iq, dq, sq, mq, st, dt;
    static const char* optionalQVTags[];
    static const char* optionalQVNames[];

    //
    // Initialize all optional fields.  Required fields will be
    // assigned a value later.
    //
    SAMAlignment();

    void PrintSAMAlignment(std::ostream& out = std::cout);

    // Find position of the nth character in a string.
    size_t FindPosOfNthChar(std::string str, int n, char c);

    // Trim the end '\n\r' characters from a string.
    std::string TrimStringEnd(std::string str);

    bool StoreValues(std::string& line, int lineNumber = 0);

    // CopyQVs writes the strings from the optional QV tags to a vector. The
    // order of QVs in the vector is given by optionalQVNames[]
    void CopyQVs(std::vector<std::string>* optionalQVs);
};

class SAMPosAlignment : public SAMAlignment
{
public:
    unsigned int qStart, qEnd;
    unsigned int tStart, tEnd;
    int qStrand, tStrand;
};

#endif