SnipParser.cpp

#include "SnipParser.h"

//SNP in human genome 10430639. 
struct ST
{
    int rs;       // RS number
    char ch[4];   // Chromosone
    int pos;      // Position
    char a;       // first nucleotide
    char b;       // second nucleotide
} sname;

struct SM
{
    int rs;       // RS number
    char a;       // first nucleotide
    char b;       // second nucleotide
} smerge;

std::vector<ST> snp(10430639);
std::vector<SM> snpM(10430639);

// Use 'variant::index' to know the type strored in variant (zero-based index). 
//Read an Ancestory.com/23t0me and FtDNA RAW DNA file and create a 'standard array'
bool  SnipParser::Ancestory(wchar_t* fi_)
{
  
    //std::fstream  fs(fi_, std::ios_base::in | std::ios_base::binary);
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        int noreadcount = 0;
        bool noY = true;
        //Open file for read 
        fs.open(fi_, std::ios::in);
        //Check file was opened  
        if (fs.is_open()) {
            int inx = 0;
            //START: reset loadcount_ and vector for next file for next file
            loadCount_ = 0;
            snp.clear();
            snp.resize(10430639);
            //END: reset loadcount_ and vector for next file for next file
            wcscpy_s(fileLoaded_,fi_); //store latest filename
            while (!fs.eof())
            {
                //read a line into a temorary buffer
                fs.getline(nbuffer, 256);
                int rdindex = 0;
                
                //GET RS Number numeric part only
                if (nbuffer[rdindex] == 'r' && nbuffer[rdindex +1] == 's' && isdigit((int)nbuffer[rdindex +2])) {
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    num[0] = NULL;
                    rdindex += 2;
                    while (isdigit((int)nbuffer[rdindex]) && rdindex < 23)
                    {
                        num[nmindex] = nbuffer[rdindex];
                        rdindex++;
                        nmindex++;
                    }
                    num[nmindex] = NULL;
                    //First in the line is the RS number
                    snp[inx].rs = atoi(num);
                    //move past tab or spaces to next numeric data chromosone number
                    while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                    {//wrote whith braces for readablility
                        rdindex++;
                    }
                    //re-init 
                    nmindex = 0;
                    num[0] = NULL;

                    // 23 is the X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.
                    if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                    {
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        //second in the line is the chromosone number
                        num[nmindex] = NULL;
                        strcpy_s(snp[inx].ch, num);
                    }

                    //move past tab or spaces to next numeric data position number
                    while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                    {//wrote whith braces for readablility
                        rdindex++;
                    }
                    //read position
                    //re-init 
                    nmindex = 0;
                    num[0] = NULL;
                    while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                    {
                        num[nmindex] = nbuffer[rdindex];
                        rdindex++;
                        nmindex++;
                    }
                    num[nmindex] = NULL;
                    //second in the line is the chromosone number
                    snp[inx].pos = atoi(num);

                    //As the last two values are not numeric we have to rely on the file still being TAB delimited
                    while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                        && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '0' && nbuffer[rdindex] != '-' && rdindex < 256)
                    {
                        rdindex++;
                    }
                    snp[inx].a = nbuffer[rdindex];
                    rdindex++;
                    //As the last two values are not numeric we have to rely on the file still being TAB delimited
                    while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                        && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '0' && nbuffer[rdindex] != '-' && rdindex < 256)
                    {
                        rdindex++;
                    }
                    //Is Char
                    snp[inx].b = nbuffer[rdindex];
                    //Determine Sex
                    if ((snp[inx].ch[0] == '2' && snp[inx].ch[1] == '4') && snp[inx].a == '0' && snp[inx].b == '0') noreadcount++;
                    if (noY == true && (snp[inx].ch[0] == '2' && snp[inx].ch[1] == '4'))
                    {
                        noY = false;
                    }
                    if (noreadcount > 15 || noY == true) sex_ = 'F';
                    else sex_ = 'M';
                    //Determine Sex
                    //increment the primary index
                    inx++;
                    //increment count of lines loaded
                    loadCount_++;
                }
                else 
                {
                    for (int indx = 0; indx < 255; indx++)
                    {
                        if ((nbuffer[indx] == 'U' && nbuffer[indx + 1] == 'I' && nbuffer[indx + 2] == 'L' && nbuffer[indx + 3] == 'D') || (nbuffer[indx] == 'u' && nbuffer[indx + 1] == 'i' && nbuffer[indx + 2] == 'l' && nbuffer[indx + 3] == 'd'))
                        {
                            for (int i = indx+3; i < indx + 12; i++)
                            {
                                if (isdigit((int)nbuffer[i]))
                                {
                                    char sub[3] = "";
                                    sub[0]=nbuffer[i]; 
                                    sub[1]=nbuffer[i + 1];
                                    sub[2] = NULL;
                                    NCBIBuild_ = sub;
                                    break;
                                }
                            }
                        }
                     }
                }
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
        }
        else false;
    }

    return true;
};
bool  SnipParser::MergeAncestory(wchar_t* fi_)
{ 
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        //merge variables
        mergefile_ = 0;
        merged_ = allcecked_ = 0;
        end_index_ = origloadcount_ = loadCount_;
        //merge variables
        //Open file for read 
        fs.open(fi_, std::ios::in);
        //Check file was opened  
        if (fs.is_open()) {
            int inx = loadCount_ + 1,rst, rdindex = 0;
            //NO!!!: reset loadcount_ and vector for next file for next file
            wcscpy_s(fileLoaded_, fi_); //store latest filename
            nbuffer[257] = NULL;        //more efficient
            std::string vercheck;       //more efficient
            initMergeCopy();            //create merge subset
            while (!fs.eof() && !abortMerge_)
            {   //read a line into a temporary buffer
                fs.getline(nbuffer, 256);
                //Merge code
                vercheck = nbuffer;
                //Merge code
                rdindex = 0;
                //GET RS Number numeric part only
                if (nbuffer[rdindex] == 'r' && nbuffer[rdindex + 1] == 's' && isdigit((int)nbuffer[rdindex + 2])) {
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    num[0] = NULL;
                    rdindex += 2;
                    while (isdigit((int)nbuffer[rdindex]) && rdindex < 23)
                    {
                        num[nmindex] = nbuffer[rdindex];
                        rdindex++;
                        nmindex++;
                    }
                    num[nmindex] = NULL;
                    mergefile_++; //get the total merge import count so a percentage difference can be calculated
                    //First in the line is the RS number
                    rst = atoi(num);
                    if (mergeRs(rst, vercheck))
                    {
                        snp[inx].rs = rst;
                        //move past tab or spaces to next numeric data chromosone number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;

                        // 23 is the X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.
                        if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                        {
                            while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                            {
                                num[nmindex] = nbuffer[rdindex];
                                rdindex++;
                                nmindex++;
                            }
                            //second in the line is the chromosone number
                            num[nmindex] = NULL;
                            strcpy_s(snp[inx].ch, num);
                        }

                        //move past tab or spaces to next numeric data position number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //read position
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //second in the line is the chromosone number
                        snp[inx].pos = atoi(num);

                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '0' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        snp[inx].a = nbuffer[rdindex];
                        rdindex++;
                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '0' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        //Is Char
                        snp[inx].b = nbuffer[rdindex];
                    }//END MERGE SCOPE!
                    //increment the primary index
                    inx++;
                    //increment count of lines loaded
                    loadCount_++;
                }
                else
                {
                    for (int indx = 0; indx < 255; indx++)
                    {
                        if ((nbuffer[indx] == 'U' && nbuffer[indx + 1] == 'I' && nbuffer[indx + 2] == 'L' && nbuffer[indx + 3] == 'D') || (nbuffer[indx] == 'u' && nbuffer[indx + 1] == 'i' && nbuffer[indx + 2] == 'l' && nbuffer[indx + 3] == 'd'))
                        {
                            for (int i = indx + 3; i < indx + 12; i++)
                            {
                                if (isdigit((int)nbuffer[i]))
                                {
                                    char sub[3] = "";
                                    sub[0] = nbuffer[i];
                                    sub[1] = nbuffer[i + 1];
                                    sub[2] = NULL;
                                    NCBIBuild_ = sub;
                                    break;
                                }
                            }
                        }
                    }
                }
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
         
        }
        else false;
    }
    //merge failed
    if (abortMerge_) {
        revertMerge();
        return false;
    }
    
    return true;
}

//FTDNA has VG numbers that may corespond to RS numbers
bool  SnipParser::FTDNA(wchar_t* fi_)
{
    //std::fstream  fs(fi_, std::ios_base::in | std::ios_base::binary);
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        int VG = 0; //illumina
        //Open file for read 
        fs.open(fi_, std::ios::in);
        //Check file was opened  
        if (fs.is_open()) {
            int inx = 0;
            int fdind = 0; //ftdna-illumina
            //START: reset loadcount_ and vector for next file for next file
            loadCount_ = 0;
            sex_ = 'F'; //Set sex to female will change if 'Y' is found!
            //Illumina unloaded count
            illuminaU_ = illuminaT_ = 0; //Reset Transaled / Untransalated counts
            snp.clear();
            snp.resize(10430639);
            wcscpy_s(fileLoaded_, fi_); //store latest filename
            //END: reset loadcount_ and vecotr for next file for next file
            while (!fs.eof())
            {
                fdind = 0;
                //read a line into a temorary buffer
                fs.getline(nbuffer, 256);
                int rdindex = 2;
                if (nbuffer[fdind] == '\"') fdind++; //ftdna-illumina
                //GET RS Number numeric part only 

                if (((nbuffer[fdind] == 'r' && nbuffer[fdind + 1] == 's') || (nbuffer[fdind] == 'V' && nbuffer[fdind + 1] == 'G')) && isdigit((int)nbuffer[fdind + 2]))
                {//ftdna-illumina
                    int ftdna = 0;
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    rdindex += fdind;//ftdna-illumina
                    num[0] = NULL;

                    if (nbuffer[fdind] == 'r' && nbuffer[fdind + 1] == 's')
                    {
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //First in the line is the RS number
                        snp[inx].rs = atoi(num);

                    }
                    else
                    {
                        //FTDNA MyHeritage name : VG01S1077  VG Chromosone number S numeric  rs77931234
                        nmindex = 0;
                        if (nbuffer[fdind] == 'V' && nbuffer[fdind + 1] == 'G')
                        {
                            fdind += 2; //Get first chromosone digit
                            num[nmindex] = nbuffer[fdind];
                            nmindex++;
                            fdind++; //Get second chromosone digit
                            num[nmindex] = nbuffer[fdind];
                            nmindex++;
                            fdind++;
                            fdind++; //Skip Alpha char
                        }
                        while (isdigit((int)nbuffer[fdind]) && fdind < 24)
                        {
                            num[nmindex] = nbuffer[fdind];
                            fdind++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        rdindex =fdind;                  //set read index
                        snp[inx].rs = FTDNADecode(num); //ver 0.3 beta separate decode function!
                    }
                 if (snp[inx].rs > 0) //stop line load of uniterpreted VG codes
                 {

                   //move past tab or spaces to next numeric data chromosone number
                   while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nbuffer[rdindex] != 'X' && nbuffer[rdindex] != 'Y' && nbuffer[rdindex] != 'x' && nbuffer[rdindex] != 'y')
                    {//wrote whith braces for readablility
                            rdindex++;
                    }
                    //re-init 
                    nmindex = 0;
                    num[0] = NULL;

                    if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                    {
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        //second in the line is the chromosone number
                        num[nmindex] = NULL;
                        strcpy_s(snp[inx].ch, num);
                    }
                    else {
                        snp[inx].ch[0] = nbuffer[rdindex]; //X & Y sinle char so why waste a strcpy call!
                        if (snp[inx].ch[0] == 'x') snp[inx].ch[0] = 'X'; //paranoia cass fix
                        if (snp[inx].ch[0] == 'y') snp[inx].ch[0] = 'Y'; //paranoia cass fix
                        snp[inx].ch[1] = NULL;

                    }
                    
                    //move past tab or spaces to next numeric data posotion number
                    while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                    {//wrote whith braces for readablility
                        rdindex++;
                    }
                    //read position
                        //re-init 
                    nmindex = 0;
                    num[0] = NULL;
                    while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                    {
                        num[nmindex] = nbuffer[rdindex];
                        rdindex++;
                        nmindex++;
                    }
                    num[nmindex] = NULL;
                    //second in the line is the chromosone number
                    snp[inx].pos = atoi(num);
     

                    //As the last two values are not numeric we have to rely on the file still being TAB delimited
                    while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                        && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                    {
                        rdindex++;
                    }
                    snp[inx].a = nbuffer[rdindex];
                    //make '0' our standard for noread
                    if (snp[inx].a == '-') snp[inx].a = '0';
                    rdindex++;
                    //As the last two values are not numeric we have to rely on the file still being TAB delimited
                    while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                        && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                    {
                        rdindex++;
                    }
                    //Is Char
                    snp[inx].b = nbuffer[rdindex];
                    //make '0' our standard for noread
                    if (snp[inx].b == '-') snp[inx].b = '0';
                    //increment the primary index
                     //Move Sex check here
                    if (snp[inx].ch[0] == 'Y' && snp[inx].a != '0') {
                        sex_ = 'M';
                    }
                    inx++;
                    //increment count of lines loaded
                    loadCount_++;

                }
            } //FTDNA do not ref NCBI build
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
        }
        else false;
    }

    return true;
};
//MergeFTDNA
//FTDNA has VG numbers that may corespond to RS numbers
bool  SnipParser::MergeFTDNA(wchar_t* fi_)
{  
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        int VG = 0; //illumina
        //Open file for read 
        fs.open(fi_, std::ios::in);
        if (fs.is_open()) {
        //Check file was opened  
            int fdind = 0; //ftdna-illumina
            //merge variables
            mergefile_ = 0;
            merged_ = allcecked_ = 0;
            end_index_ = origloadcount_ = loadCount_;
            abortMerge_ = false;
            //merge variables
            sex_ = 'F'; //Set sex to female will change if 'Y' is found!
            //Illumina unloaded count
            illuminaU_ = illuminaT_ = 0; //Reset Transaled / Untransalated counts
            snp.resize(10430639);
            int inx = loadCount_ + 1, rst, rdindex = 0;  //merge code
            wcscpy_s(fileLoaded_, fi_); //store latest filename
            nbuffer[257] = NULL;        //more efficient
            std::string vercheck;       //more efficient
            initMergeCopy();            //create merge subset
            //END:
            while (!fs.eof() && !abortMerge_)
            {
                fdind = 0;
                //read a line into a temorary buffer
                fs.getline(nbuffer, 256);
                //Merge code
                vercheck = nbuffer;
                //Merge code
                int rdindex = 2;
                if (nbuffer[fdind] == '\"') fdind++; //ftdna-illumina
                //GET RS Number numeric part only 

                if (((nbuffer[fdind] == 'r' && nbuffer[fdind + 1] == 's') || (nbuffer[fdind] == 'V' && nbuffer[fdind + 1] == 'G')) && isdigit((int)nbuffer[fdind + 2]))
                {//ftdna-illumina
                    int ftdna = 0;
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    rdindex += fdind;//ftdna-illumina
                    num[0] = NULL;

                    if (nbuffer[fdind] == 'r' && nbuffer[fdind + 1] == 's')
                    {
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //First in the line is the RS number
                        rst = atoi(num);

                    }
                    else
                    {
                        //FTDNA MyHeritage name : VG01S1077  VG Chromosone number S numeric  rs77931234
                        nmindex = 0;
                        if (nbuffer[fdind] == 'V' && nbuffer[fdind + 1] == 'G')
                        {
                            fdind += 2; //Get first chromosone digit
                            num[nmindex] = nbuffer[fdind];
                            nmindex++;
                            fdind++; //Get second chromosone digit
                            num[nmindex] = nbuffer[fdind];
                            nmindex++;
                            fdind++;
                            fdind++; //Skip Alpha char
                        }
                        while (isdigit((int)nbuffer[fdind]) && fdind < 24)
                        {
                            num[nmindex] = nbuffer[fdind];
                            fdind++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        rdindex = fdind;                  //set read index
                        rst = FTDNADecode(num); //ver 0.3 beta separate decode function!
                    }
                    if (rst > 0 && mergeRs(rst, vercheck)) //stop line load of uniterpreted VG codes
                    {
                        snp[inx].rs = rst;
                        //move past tab or spaces to next numeric data chromosone number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nbuffer[rdindex] != 'X' && nbuffer[rdindex] != 'Y' && nbuffer[rdindex] != 'x' && nbuffer[rdindex] != 'y')
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;

                        if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                        {
                            while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                            {
                                num[nmindex] = nbuffer[rdindex];
                                rdindex++;
                                nmindex++;
                            }
                            //second in the line is the chromosone number
                            num[nmindex] = NULL;
                            strcpy_s(snp[inx].ch, num);
                        }
                        else {
                            snp[inx].ch[0] = nbuffer[rdindex]; //X & Y sinle char so why waste a strcpy call!
                            if (snp[inx].ch[0] == 'x') snp[inx].ch[0] = 'X'; //paranoia cass fix
                            if (snp[inx].ch[0] == 'y') snp[inx].ch[0] = 'Y'; //paranoia cass fix
                            snp[inx].ch[1] = NULL;

                        }

                        //move past tab or spaces to next numeric data posotion number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //read position
                            //re-init 
                        nmindex = 0;
                        num[0] = NULL;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //second in the line is the chromosone number
                        snp[inx].pos = atoi(num);

                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        snp[inx].a = nbuffer[rdindex];
                        //make '0' our standard for noread
                        if (snp[inx].a == '-') snp[inx].a = '0';
                        rdindex++;
                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        //Is Char
                        snp[inx].b = nbuffer[rdindex];
                        //make '0' our standard for noread
                        if (snp[inx].b == '-') snp[inx].b = '0';
                        //increment the primary index
                        inx++;
                        //increment count of lines loaded
                        loadCount_++;

                    }
                } //FTDNA do not ref NCBI build
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
        }
        else false;
    }

    return true;
};

//23andMe function
//has VG numbers that may corespond to RS numbers
bool  SnipParser::f23andMe(wchar_t* fi_)
{
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        bool singleAllele;
        //Open file for read 
        fs.open(fi_, std::ios::in);
        //Check file was opened  
        if (fs.is_open()) {
            int inx = 0;
            singleAllele = false;
            //START: reset loadcount_ and vector for next file for next file
            loadCount_ = 0;
            sex_ = 'F'; //Set sex to female will change if 'Y' is found!
            //Illumina unloaded count
            illuminaU_ = illuminaT_ = 0; //Reset Transaled / Untransalated counts
            snp.clear();
            snp.resize(10430639);
            wcscpy_s(fileLoaded_, fi_); //store latest filename
            //END: reset loadcount_ and vector for next file for next file
            while (!fs.eof())
            {
                //read a line into a temorary buffer
                fs.getline(nbuffer, 256);
                int rdindex = 0;
                //GET RS Number numeric part only 
                if (((nbuffer[rdindex] == 'r' && nbuffer[rdindex + 1] == 's') || (nbuffer[rdindex] == 'i' && isdigit((int)nbuffer[rdindex + 1]) )) && isdigit((int)nbuffer[rdindex + 2]))
                {//ftdna-illumina
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    num[0] = NULL;

                    if (nbuffer[rdindex] == 'r' && nbuffer[rdindex + 1] == 's')
                    {
                        rdindex += 2;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //First in the line is the RS number
                        snp[inx].rs = atoi(num);

                    }
                    else
                    {
                        //23toMe ixxxx codes ro rsxxx codes
                        int isw = 0;
                        nmindex = 0;
                        rdindex += 1; //Skip i
                                               
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                       
                        snp[inx].rs = f23andMeDecode(num);//in example  VG01S1077 ftdna will equal numeric 11007
                    }

                    if (snp[inx].rs > 0) //stop line load of uniterpreted i codes
                    {
                        //move past tab or spaces to next numeric data chromosone number below bug fix 3/11/21
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nbuffer[rdindex] != 'X' && nbuffer[rdindex] != 'Y' && nbuffer[rdindex] != 'x' && nbuffer[rdindex] != 'y' && nbuffer[rdindex] != 'm' && nbuffer[rdindex] != 'M')
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;

                        if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                        {
                            while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                            {
                                num[nmindex] = nbuffer[rdindex];
                                rdindex++;
                                nmindex++;
                            }
                            //second in the line is the chromosone number
                            num[nmindex] = NULL;
                            strcpy_s(snp[inx].ch, num);
                        }
                        else {//Bug fix 3/10/21
                               if((nbuffer[rdindex] == 'M' && nbuffer[rdindex + 1] == 'T') || (nbuffer[rdindex] == 'm' && nbuffer[rdindex + 1] == 't'))
                                 {//know its uppercase but others use the format
                                  snp[inx].ch[0] = 'M';
                                  snp[inx].ch[1] = 'T';
                                  snp[inx].ch[2] = NULL;  //Bug fix 3/11/21
                                  singleAllele = true;
                                 } else
                                       {
                                        snp[inx].ch[0] = nbuffer[rdindex]; 
                                        if (snp[inx].ch[0] == 'x') snp[inx].ch[0] = 'X'; //paranoia cass fix
                                        if (snp[inx].ch[0] == 'y') snp[inx].ch[0] = 'Y'; //paranoia cass fix
                                        snp[inx].ch[1] = NULL;
                                        singleAllele = true;
                                       }

                        }

                        //move past tab or spaces to next numeric data posotion number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //read position
                            //re-init 
                        nmindex = 0;
                        num[0] = NULL;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //second in the line is the chromosone number
                        snp[inx].pos = atoi(num);


                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        snp[inx].a = nbuffer[rdindex];
                        //make '0' our standard for noread
                        if (snp[inx].a == '-') snp[inx].a = '0';
                        rdindex++;
                        if (singleAllele)
                        {
                            snp[inx].b = NULL;
                        }
                        else
                        {
                            //As the last two values are not numeric we have to rely on the file still being TAB delimited
                            while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                                && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                            {
                                rdindex++;
                            }
                            //Is Char
                            snp[inx].b = nbuffer[rdindex];
                            //make '0' our standard for noread
                            if (snp[inx].b == '-') snp[inx].b = '0';
                        }
                        //Move Sex check here
                        if (snp[inx].ch[0] == 'Y' && snp[inx].a != '0') {
                            sex_ = 'M';
                        }
                        //increment the primary index
                        inx++;
                        //increment count of lines loaded
                        loadCount_++;

                    }
                }
                //does not ref ncbi build
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
        }
        else false;
    }
    return true;
};
//Merge 23toMe
//23andMe function
//has VG numbers that may corespond to RS numbers
bool  SnipParser::Mergef23andMe(wchar_t* fi_)
{
    std::fstream  fs;
    if (!fs.bad())
    {
        char nbuffer[260];
        int loopbreak = 0;
        //merge variables
        mergefile_ = 0;
        merged_ = allcecked_ = 0;
        end_index_ = origloadcount_ = loadCount_;
        //merge variables
        bool singleAllele;
        //Open file for read 
        fs.open(fi_, std::ios::in);
        //Check file was opened  
        if (fs.is_open()) {
            singleAllele = false;
            sex_ = 'F'; //Set sex to female will change if 'Y' is found!
            //Illumina unloaded count
            illuminaU_ = illuminaT_ = 0; //Reset Transaled / Untransalated counts
            snp.resize(10430639);
            //NO!!!: reset loadcount_ and vector for next file for next file
            int inx = loadCount_ + 1, rst, rdindex = 0;  //merge code
            wcscpy_s(fileLoaded_, fi_); //store latest filename
            nbuffer[257] = NULL;        //more efficient
            std::string vercheck;       //more efficient
            initMergeCopy();            //create merge subset
            //END:
            while (!fs.eof() && !abortMerge_)
            {
                //read a line into a temorary buffer
                fs.getline(nbuffer, 256);
                //Merge code
                vercheck = nbuffer;
                //Merge code
                int rdindex = 0;
                //GET RS Number numeric part only 
                if (((nbuffer[rdindex] == 'r' && nbuffer[rdindex + 1] == 's') || (nbuffer[rdindex] == 'i' && isdigit((int)nbuffer[rdindex + 1]))) && isdigit((int)nbuffer[rdindex + 2]))
                {//ftdna-illumina
                    char num[20];
                    int  nmindex = 0;
                    loopbreak = 0;
                    num[0] = NULL;

                    if (nbuffer[rdindex] == 'r' && nbuffer[rdindex + 1] == 's')
                    {
                        rdindex += 2;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //First in the line is the RS number
                         rst = atoi(num);

                    }
                    else
                    {
                        //23toMe ixxxx codes ro rsxxx codes
                        int isw = 0;
                        nmindex = 0;
                        rdindex += 1; //Skip i

                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 24)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;

                        rst = f23andMeDecode(num);//in example  VG01S1077 ftdna will equal numeric 11007
                    }

                    if (rst > 0 && mergeRs(rst, vercheck)) //stop line load of uniterpreted i codes
                    {
                        snp[inx].rs = rst;
                        //move past tab or spaces to next numeric data chromosone number below bug fix 3/11/21
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nbuffer[rdindex] != 'X' && nbuffer[rdindex] != 'Y' && nbuffer[rdindex] != 'x' && nbuffer[rdindex] != 'y' && nbuffer[rdindex] != 'm' && nbuffer[rdindex] != 'M')
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;

                        if (isdigit((int)nbuffer[rdindex])) //if autosomal chr
                        {
                            while (isdigit((int)nbuffer[rdindex]) && rdindex < 256 && nmindex < 3)//last clause is to prevent overflow on corrupt file
                            {
                                num[nmindex] = nbuffer[rdindex];
                                rdindex++;
                                nmindex++;
                            }
                            //second in the line is the chromosone number
                            num[nmindex] = NULL;
                            strcpy_s(snp[inx].ch, num);
                        }
                        else {//Bug fix 3/10/21
                            if ((nbuffer[rdindex] == 'M' && nbuffer[rdindex + 1] == 'T') || (nbuffer[rdindex] == 'm' && nbuffer[rdindex + 1] == 't'))
                            {//know its uppercase but others use the format
                                snp[inx].ch[0] = 'M';
                                snp[inx].ch[1] = 'T';
                                snp[inx].ch[2] = NULL;  //Bug fix 3/11/21
                                singleAllele = true;
                            }
                            else
                            {
                                snp[inx].ch[0] = nbuffer[rdindex];
                                if (snp[inx].ch[0] == 'x') snp[inx].ch[0] = 'X'; //paranoia cass fix
                                if (snp[inx].ch[0] == 'y') snp[inx].ch[0] = 'Y'; //paranoia cass fix
                                snp[inx].ch[1] = NULL;
                                singleAllele = true;
                            }

                        }

                        //move past tab or spaces to next numeric data posotion number
                        while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {//wrote whith braces for readablility
                            rdindex++;
                        }
                        //read position
                        //re-init 
                        nmindex = 0;
                        num[0] = NULL;
                        while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                        {
                            num[nmindex] = nbuffer[rdindex];
                            rdindex++;
                            nmindex++;
                        }
                        num[nmindex] = NULL;
                        //second in the line is the chromosone number
                        snp[inx].pos = atoi(num);

                        //As the last two values are not numeric we have to rely on the file still being TAB delimited
                        while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                            && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                        {
                            rdindex++;
                        }
                        snp[inx].a = nbuffer[rdindex];
                        //make '0' our standard for noread
                        if (snp[inx].a == '-') snp[inx].a = '0';
                        rdindex++;
                        if (singleAllele)
                        {
                            snp[inx].b = NULL;
                        }
                        else
                        {
                            //As the last two values are not numeric we have to rely on the file still being TAB delimited
                            while (nbuffer[rdindex] != 'A' && nbuffer[rdindex] != 'C' && nbuffer[rdindex] != 'G' && nbuffer[rdindex] != 'T'
                                && nbuffer[rdindex] != 'D' && nbuffer[rdindex] != 'I' && nbuffer[rdindex] != '-' && rdindex < 256)
                            {
                                rdindex++;
                            }
                            //Is Char
                            snp[inx].b = nbuffer[rdindex];
                            //make '0' our standard for noread
                            if (snp[inx].b == '-') snp[inx].b = '0';
                        }
                        //increment the primary index
                        inx++;
                        //increment count of lines loaded
                        loadCount_++;
                    }
                }
                //does not ref ncbi build
                loopbreak++;
                if (loopbreak == 2000) break;
            }
            fs.close();
        }
        else false;
    }
    return true;
};

//Return the number of translated VG codes
unsigned int  SnipParser::IllumTransVG(void)
{
    return illuminaT_;
}
//Return the number of untranslated VG codes
unsigned int  SnipParser::IllumUntransVG(void)
{
    return illuminaU_;
}
//return the number of lines loaded
int SnipParser::SNPCount(void)
{
    return loadCount_;
}
//return sex
wchar_t SnipParser::sex(void)
{
    return sex_;
}
unsigned int SnipParser::merged(void)
{
    return merged_;
}

//make merge copy
void SnipParser::initMergeCopy(void)
{
    if (loadCount_ > 0) {
        for (unsigned int i = 0; i <= loadCount_; i++) {
            snpM[i].rs = snp[i].rs;
            snpM[i].a  = snp[i].a;
            snpM[i].b  = snp[i].b;
        }
    }
    snpM.resize(loadCount_ + 16); //add 16 for paranoia
    return;
}
//returns if merge failed
bool SnipParser::MergeState(void)
{
    return abortMerge_;
}
/*Revert a failed merge*/
void SnipParser::revertMerge(void)
{
    //Reset rsid to null
    for (unsigned int i = 1 + origloadcount_; i < loadCount_; i++)
    {
        snp[i].rs = NULL;
    }
    //reset load count
    loadCount_ = origloadcount_;

}
unsigned int SnipParser::MergeProcessed(void)
{
    return(allcecked_ + merged_);
}

/*Check the subject is the same to prevent the generation of garbage genetic files
Even though this is the most effiecent self resizing inlined loop I could write
the shear amount of comparisons involved in unsorted data makes this a slow job!! */
__forceinline bool SnipParser::mergeRs(int code,std::string line)
{
    for (unsigned int i = 0; i <= end_index_;)
    { //merge if code is a no read or not found
        if (snpM[i].rs == code)
        {           
            allcecked_++;
            //special case replace noread value
            if (snpM[i].a == '0') return true;
            std::size_t found = line.find(snpM[i].a);
            if (found == std::string::npos) failcheck_++;
            else { 
                  found = line.find(snpM[i].b);
                  if (found == std::string::npos) failcheck_++;
                 }
            //shorten the loop with every match we can move data aroud as its a subset copy!
            snpM[i].rs = snpM[end_index_].rs;
            snpM[i].a = snpM[end_index_].a;
            snpM[i].b = snpM[end_index_].b;
            end_index_--;
            if (allcecked_ > 1250)
            { //if all matches are less that 1/4 of the total check the files are way to different and merge is aborted
                if ((allcecked_ >> 2) < failcheck_) abortMerge_ = true;
            }
            return false;
        }
        //inceament loop
        i++;
    }
    merged_++;
    return true;
}
/*RS number search function passed the RS number to searcg for
and a structure of type s to place the data in if a match is found */
bool SnipParser::RsSearch(int *rs, char* chr1, char* chr2, char* chr3, char* chr4, int *pos, char *a, char *b)
{
    // Check you have SNP data loaded
    if (loadCount_ > 0)
    { 
        // Search for RS numer int rs
        for (unsigned int i = 0; i <=loadCount_;)
        {
            if (snp[i].rs == *rs)
            {
                //match found! populate and return the structure
                *rs = snp[i].rs;         // RS number
                *chr1 = snp[i].ch[0];    // Chromosone array as string
                *chr2 = snp[i].ch[1];    // Chromosone array as string
                *chr3 = snp[i].ch[2];    // Chromosone array as string
                *chr4 = snp[i].ch[3];    // Chromosone array as string
                *pos = snp[i].pos;       // Position
                *a = snp[i].a;           // first nucleotide
                *b = snp[i].b;           // first nucleotide
                
                //START: For Ancestory DNA files 23 is the X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.
                if (*chr1 == '2' && *chr2 == '3')
                {
                    *chr1 = 'X';
                    *chr2 = NULL;
                }
                if (*chr1 == '2' && *chr2 == '4')
                {
                    *chr1 = 'Y';
                    *chr2 = NULL;
                }
                if (*chr1 == '2' && *chr2 == '5')
                {
                    *chr1 = 'P';
                    *chr2 = 'A';
                    *chr3 = 'R';
                    *chr4 = NULL;
                }
                if (*chr1 == '2' && *chr2 == '6')
                {
                    *chr1 = 'm';
                    *chr2 = 't';
                    *chr3 = NULL;
                }
                //END: For Ancestory DNA files 23 is the X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.
                return true;
            }
            //inceament loop
            i++;
        }

    }
    return false;
}

//return version number
std::string  SnipParser::PVer(void)
{
    return  Pversion_;
}

/*return the NCBI Build the file was based on gives position a referance
  as well as being a clue to the age of the files contents */
std::string SnipParser::NCBIBuild(void)
{
    return NCBIBuild_;
}
/*Major Work in porgress*/
bool  SnipParser::AncestoryWriter(wchar_t* fi_)
{
     std::fstream  fs;
     if (!fs.bad())
     {
         char timebufd[128], timebuft[128];
         std::string  lbuffer;
         std::time_t t = std::time(nullptr);
         int loopbreak = 0;
         // Convert the wchar_t string to a char* string. Record
         // the length of the original string and add 1 to it to
         // account for the terminating null character.
         size_t origsize = wcslen(fileLoaded_) + 1;
         size_t convertedChars = 0;
        //MS example code
         char strConcat[] = " (char *)";
         size_t strConcatsize = (strlen(strConcat) + 1) * 2;
         const size_t newsize = origsize * 2;
         char* nstring = new char[newsize + strConcatsize];
         wcstombs_s(&convertedChars, nstring, newsize, fileLoaded_, _TRUNCATE);
          //Open file for write 
         fs.open(fi_, std::ios::out);
         //Check file was opened  
         if (fs.is_open()) {
             int unsigned inx = 0;
             //Start:Write Header
             _tzset(); //set timezone
             _strtime_s(timebuft, 128);
             _strdate_s(timebufd, 128);
             /*Write an infomative header close to the orgiginal ver 1,0 ancestry header but without the ref genome as it will change file to file
             and with the program name ver and file creation date as well as the original input file name and path*/
             lbuffer = "#File Format AncestryDNA(c) raw data download\n";
             lbuffer += "#This file was generated by ParseSNP version: " + Pversion_ + " at " + timebufd + " " + timebuft + "\n";
             lbuffer += "#Forth line down is that below which some progarms may read to get format verion!!! Futureproofing\n";
             lbuffer += "#Data is formatted using AncestryDNA converter version: V1.0\n";
             lbuffer += "#Original rsID datafile: ";
             lbuffer += nstring;
             lbuffer += "\n";
             lbuffer += "Ancestory DNA  23 is X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.";
             lbuffer += "#Genetic data is provided below as five TAB delimited columns.\n" ;
             lbuffer += "#Each line corresponds to a SNP.Column one provides the SNP identifier rsID.\n";
             lbuffer += "#Columns two and three contain the chromosome and basepair position\n";
             lbuffer += "#of the SNP using a human reference build coordinates.Columns four and five\n";
             lbuffer += "#contain the two alleles observed at this SNP(genotype).The genotype is reported\n";
             lbuffer += "#on the forward(+) strand with respect to the human reference.\n";
             lbuffer += "   rsID    Chromosome  Position    Allele1 Allele2\n";
             const char* write_it = lbuffer.c_str();
             fs.write(write_it, lbuffer.length());
             //End:Write Header
             char c_num[50] = {'0'};//Added 0 padding as NULL terminator
             bool over22;
             std::string rsID, Position, Chromosome,allele1,allele2;
             while (inx < loadCount_)
             {   //For Ancestory DNA files 23 is the X, 24 is Y, 25 is the (Pseudoautosomal region) PAR region, and 26 is mtDNA.
                 over22 = false;
                 if (!_itoa_s(snp[inx].rs, c_num, 10)) rsID = (std::string) c_num;  //warning C6054 ignore _itoa_s returns a NULL terminated sting
                 else break;
                 //convert 23toMe
                 if (!strcmp(snp[inx].ch, "MT")) {
                     Chromosome = (std::string)"26";
                     over22 = true;
                 }  else
                     if (!strcmp(snp[inx].ch, "X")) {
                         Chromosome = (std::string)"23";
                         over22 = true;
                     } else if (!strcmp(snp[inx].ch, "Y")) {
                         Chromosome = (std::string)"24";
                         over22 = true;
                     } else                 
                     {   //DEBUG
                         if (isdigit(atoi(snp[inx].ch)))
                         {
                             int x = 23;
                         }
                         //DEBUG
                       Chromosome = (std::string)(snp[inx].ch);
                      }
                    
                 if(!_itoa_s(snp[inx].pos, c_num, 10)) Position = c_num;
                 else break;
                 if (over22)
                 { //ancestory's wierd to bases for X Y and MT where there is only 1
                   // '-' as been converted on load but I am leaving the '-' option for any future code that the conversion is omitted  
                     if (snp[inx].a == '-' || snp[inx].a == '0')
                     {
                         allele1 = allele2 = (std::string)"0";
                     }
                     else
                     {
                         allele1 = allele2 = snp[inx].a + NULL;
                     }
                 }
                 else {
                        if (snp[inx].a == '-' || snp[inx].a == '0') allele1 = (std::string)"0";
                             else allele1 = snp[inx].a + NULL;
                        if (snp[inx].b == '-' || snp[inx].b == '0') allele2 = (std::string)"0";
                             else allele2 = snp[inx].b + NULL;
                      }

                 lbuffer = "rs" + rsID + "\t" + Chromosome + "\t" + Position + "\t" + allele1 + "\t" + allele2 + "\n";
                 //write the line
                 const char* write_it = lbuffer.c_str();
                 fs.write(write_it, lbuffer.length());
                 inx++; //increment inx to the next values / line
             }
             fs.close();
             //got through the loop assuming file wrote correctly
             return true;
         }
     }
     return false;
}
//INTERNAL code generator not of use 
void  SnipParser::FConvert(void)
{
   //std::fstream  fs(fi_, std::ios_base::in | std::ios_base::binary);
   /* wchar_t* fiIn_;
      wchar_t* fiOut_; */
    wchar_t  codeIn_[] = L"f:\\icode.txt";
    wchar_t  codeOut_[] = L"f:\\ccode.txt";

    std::fstream  fs;
    std::fstream  fsOut;
    if (!fs.bad() && !fsOut.bad())
    {
        char nbuffer[260];
        std::string  lbuffer;
        char num[100];
        int loopbreak = 0;
        int fdind = 0;
        //Open file for read 
        fs.open(codeIn_, std::ios::in);
        //Open file for write
        fsOut.open(codeOut_, std::ios::out);
        //Check file was opened  
        if (fs.is_open() && fsOut.is_open()) {
            fdind = 0;

            while (!fs.eof())
            {
                int rdindex = 0;
                int nmindex = 0;
                fs.getline(nbuffer, 256);
                //move past tab or spaces to next numeric data posotion number
                while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                {//wrote whith braces for readablility
                    rdindex++;
                }
                //read position
                //re-init 
                nmindex = 0;
                num[0] = NULL;
                while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                {
                    num[nmindex] = nbuffer[rdindex];
                    rdindex++;
                    nmindex++;
                }
                num[nmindex] = NULL;
                //START constructing the write line
                lbuffer = "case " + std::string(num) + ":" + char(13) + "  snp[inx].rs = ";
                //read second rsID number
                //move past tab or spaces to next numeric data position number
                while (!isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                {//wrote whith braces for readablility
                    rdindex++;
                }
                //read position
                //re-init 
                nmindex = 0;
                num[0] = NULL;
                while (isdigit((int)nbuffer[rdindex]) && rdindex < 256)
                {
                    num[nmindex] = nbuffer[rdindex];
                    rdindex++;
                    nmindex++;
                }
                num[nmindex] = NULL;
                //lbuffer= lbuffer + +=
                lbuffer += std::string(num) + ";" + char(13) +"  illuminaT_++;" + char(13) + "  break;" + char(13) ;
                const char* write_it = lbuffer.c_str();
                fsOut.write(write_it , lbuffer.length());
            }
        }
        fs.close();
        fsOut.close();
    }
}  
/* Searches all loaded data for matching rsID then checks for risk  allele.
If it is found it updates the odds ratio                       */
std::string SnipParser::PathogenicCall(int rsid, char riskallele, float oddsratio, float* sumoddsratio)
{
    std::string result_message = "N/A";

    // Check you have SNP data loaded
    if (loadCount_ > 0)
    {
        // Search for RS numer int rs
        for (unsigned int i = 0; i <= loadCount_;)
        {
            if (snp[i].rs == rsid)
            {    
                char buffer[8];
                char check_Y[4];
                
                if (!strcmp(snp[i].ch, "23"))
                {
                    check_Y[0] = 'X';
                    check_Y[1] = NULL;
                }
                else
                {
                    check_Y[0] = snp[i].ch[0];
                    check_Y[1] = snp[i].ch[1];
                    check_Y[2] = snp[i].ch[2];
                    check_Y[3] = snp[i].ch[3];
                }
                buffer[0] = '[';
                buffer[1] = (char)snp[i].a;
                buffer[2] = '/';
                buffer[3] = (char)snp[i].b;
                buffer[4] = ']';
                buffer[5] = ' ';
                buffer[6] = NULL;
                result_message = buffer;
               
                //Match of risk  allele on both chromosones!
                if (snp[i].a == riskallele && snp[i].b == riskallele)
                {
                    if (check_Y[0] == 'X' && sex_ == 'M') 
                    {
                        buffer[3] = '-';
                        result_message = buffer;
                        result_message += "Risk Heterozygous";
                        if (*sumoddsratio == 0.0) *sumoddsratio = oddsratio;
                        else *sumoddsratio += (float)(*sumoddsratio * oddsratio) / (float)((*sumoddsratio + 1) * (oddsratio + 1) - ((*sumoddsratio * oddsratio)));
                        return result_message;
                    }
                    result_message += "Risk Homozygous!";
                    //from a post on statistics here https://stats.stackexchange.com/questions/187107/can-you-add-up-different-genes-odds-ratios-to-get-a-general-odds-ratio
                    if (*sumoddsratio == 0.0) *sumoddsratio = oddsratio;
                    else  *sumoddsratio += (float)(*sumoddsratio * oddsratio) / (float)((*sumoddsratio + 1) * (oddsratio + 1) - ((*sumoddsratio * oddsratio)));
                    *sumoddsratio += (float)(*sumoddsratio * oddsratio) / (float)((*sumoddsratio + 1) * (oddsratio + 1) - ((*sumoddsratio * oddsratio)));
                    return result_message;
                }
                //Match in one chromosone
                if (snp[i].a == riskallele || snp[i].b == riskallele)
                {
                    result_message += "Risk Heterozygous";
                    if (*sumoddsratio == 0.0) *sumoddsratio = oddsratio;
                    else *sumoddsratio += (float)(*sumoddsratio * oddsratio) / (float)((*sumoddsratio + 1) * (oddsratio + 1) - ((*sumoddsratio * oddsratio)));
                    return result_message;
                }
                if (snp[i].a == '0' && snp[i].b == '0')  result_message += "N/A (No Read)";
                else result_message += "No Risk";
                return result_message;
            }
            //inceament loop
            i++;
        }

    }
    return result_message;
}
int SnipParser::FTDNADecode(std::string code)
{
    int rs = 0,num;

    num = atoi(code.c_str()); //in example  VG01S1077 ftdna will equal numeric 11007
    switch (num) {//rs equivelent ALL Illumina VG codes seem to realte to Cystic Fibrosis!
    case 11077:
        rs = 77931234;
        illuminaT_++;
        break;
    case 12269:
        rs = 77931234;
        illuminaT_++;
        break;
    case 11161:
        rs = 78396650;
        illuminaT_++;
        break;
    case 11154:
        rs = 74500255;
        illuminaT_++;
        break;
    case 11135:
        rs = 77829017;
        illuminaT_++;
        break;
    case 425864:
        rs = 75790268;
        break;
    case 526940:
        rs = 79967166;
        illuminaT_++;
        break;
    case 729384:
        rs = 77284892;
        illuminaT_++;
        break;
    case 729458:
        rs = 75961395;
        break;
    case 729628:
        rs = 78655421;
        illuminaT_++;
        break;
    case 744961:
        rs = 78756941;
        illuminaT_++;
        break;
    case 744986:
        rs = 77188391;
        illuminaT_++;
        break;
    case 745007:
        rs = 78440224;
        illuminaT_++;
        break;
    case 752452:
        rs = 77409459;
        illuminaT_++;
        break;
    case 729244:
        rs = 77409459;
        illuminaT_++;
        break;
    case 729268:
        rs = 79282516;
        illuminaT_++;
        break;
    case 745090:
        rs = 76713772;
        illuminaT_++;
        break;
    case 729293:
        rs = 75527207;
        illuminaT_++;
        break;
    case 729297:
        rs = 74597325;
        illuminaT_++;
        break;
    case 729341:
        rs = 75115087;
        illuminaT_++;
        break;
    case 752241:
        rs = 121908787;
        illuminaT_++;
        break;
    case 729361:
        rs = 79633941;
        illuminaT_++;
        break;
    case 750448:
        rs = 121908767;
        illuminaT_++;
        break;
    case 745132:
        rs = 76151804;
        illuminaT_++;
        break;
    case 729391:
        rs = 78194216;
        illuminaT_++;
        break;
    case 729406:
        rs = 78802634;
        illuminaT_++;
        break;
    case 729419:
        rs = 75541969;
        illuminaT_++;
        break;
    case 729422:
        rs = 79850223;
        illuminaT_++;
        break;
    case 729424:
        rs = 74767530;
        illuminaT_++;
        break;
    case 729435:
        rs = 75389940;
        illuminaT_++;
        break;
    case 752449:
        rs = 75039782;
        illuminaT_++;
        break;
    case 729444:
        rs = 74503330;
        illuminaT_++;
        break;
    case 729451:
        rs = 77010898;
        illuminaT_++;
        break;
    case 932163:
        rs = 77375493;
        illuminaT_++;
        break;
    case 931849:
        rs = 79833450;
        illuminaT_++;
        break;
    case 931531:
        rs = 77718928;
        illuminaT_++;
        break;
    case 952451:
        rs = 78340951;
        illuminaT_++;
        break;
    case 115372:
        rs = 33951465;
        illuminaT_++;
        break;
    case 128248:
        rs = 62644499;
        illuminaT_++;
        break;
    case 128239:
        rs = 5030859;
        illuminaT_++;
        break;
    case 128233:
        rs = 5030857;
        illuminaT_++;
        break;
    case 128222:
        rs = 5030856;
        illuminaT_++;
        break;
    case 128220:
        rs = 62516101;
        break;
    case 128217:
        rs = 62642937;
        illuminaT_++;
        break;
    case 128204:
        rs = 62516095;
        illuminaT_++;
        break;
    case 128194:
        rs = 62508646;
        illuminaT_++;
        break;
    case 128480:
        rs = 5030853;
        illuminaT_++;
        break;
    case 128479:
        rs = 62642933;
        illuminaT_++;
        break;
    case 128467:
        rs = 5030851;
        illuminaT_++;
        break;
    case 128449:
        rs = 62514952;
        illuminaT_++;
        break;
    case 128434:
        rs = 5030850;
        illuminaT_++;
        break;
    case 128424:
        rs = 62644503;
        illuminaT_++;
        break;
    case 128405:
        rs = 5030846;
        illuminaT_++;
        break;
    case 128402:
        rs = 62508730;
        illuminaT_++;
        break;
    case 128320:
        rs = 5030843;
        illuminaT_++;
        break;
    case 128298:
        rs = 76296470;
        illuminaT_++;
        break;
    case 128296:
        rs = 62642929;
        illuminaT_++;
        break;
    case 128223:
        rs = 62642926;
        illuminaT_++;
        break;
    case 1352444:
        rs = 76151636;
        illuminaT_++;
        break;
    case 1512228:
        rs = 78310315;
        illuminaT_++;
        break;
    case 1716802:
        rs = 28940574;
        illuminaT_++;
        break;
    case 2123270:
        rs = 5742905;
        illuminaT_++;
        break;
    default:illuminaU_++; //untranslaned lines
        break;
    }
    return rs;
}
int SnipParser::f23andMeDecode(std::string code)
{ 
    int num, rs = 0;

    num = atoi(code.c_str());
    switch (num) {//covert Illumina Internatl codes to rsID equivenelts
    case 3003626:  //CCR5 delta 32 mutation. imparts HIV1 immunity if Hetrozogous (but makes you more vunerable to flaviviruses and no immunity to HIV2
        rs = 333;
        illuminaT_++;
        break;    // All codes beyond this point are ver. 5 codes 
    case 4000478:
        rs = 118203925;
        illuminaT_++;
        break;
    case 4000479:
        rs = 62516095;
        illuminaT_++;
        break;
    case 4000481:
        rs = 62508588;
        illuminaT_++;
        break;
    case 4000635:
        rs = 121434453;
        illuminaT_++;
        break;
    case 4000834:
        rs = 199476104;
        illuminaT_++;
        break;
    case 4990151:
        rs = 111033258;
        illuminaT_++;
        break;
    case 5000002:
        rs = 121908362;
        illuminaT_++;
        break;
    case 5000003:
        rs = 111033244;
        illuminaT_++;
        break;
    case 5000043:
        rs = 200511261;
        illuminaT_++;
        break;
    case 5000047:
        rs = 369925690;
        illuminaT_++;
        break;
    case 5000119:
        rs = 879254572;
        illuminaT_++;
        break;
    case 5000064:
        rs = 80338945;
        illuminaT_++;
        break;
    case 5000092:
        rs = 121907972;
        illuminaT_++;
        break;
    case 5000121:
        rs = 199774121;
        illuminaT_++;
        break;
    case 5000142:
        rs = 749038326;
        illuminaT_++;
        break;
    case 5000663:
        rs = 3810141;
        illuminaT_++;
        break;
    case 5000693:
        rs = 111033199;
        illuminaT_++;
        break;
    case 5000696:
        rs = 111033307;
        illuminaT_++;
        break;
    case 5001996:
        rs = 80338948;
        illuminaT_++;
        break;
    case 5002001:
        rs = 104894396;
        illuminaT_++;
        break;
    case 5002096:
        rs = 267607213;
        illuminaT_++;
        break;
    case 5003116:
        rs = 121434282;
        illuminaT_++;
        break;
    case 5003117:
        rs = 121434281;
        illuminaT_++;
        break;
    case 5003700:
        rs = 121964990;
        illuminaT_++;
        break;
    case 5004213:
        rs = 121918070;
        illuminaT_++;
        break;
    case 5004778:
        rs = 74315455;
        illuminaT_++;
        break;
    case 5004781:
        rs = 74315458;
        illuminaT_++;
        break;
    case 5004790:
        rs = 74315467;
        illuminaT_++;
        break;
    case 5004829:
        rs = 121907959;
        illuminaT_++;
        break;
    case 5005735:
        rs = 104893931;
        illuminaT_++;
        break;
    case 5005799:
        rs = 119103251;
        illuminaT_++;
        break;
    case 5005800:
        rs = 119103252;
        illuminaT_++;
        break;
    case 5005927:
        rs = 80338680;
        illuminaT_++;
        break;
    case 5006058:
        rs = 121908758;
        illuminaT_++;
        break;
    case 5006076:
        rs = 121908754;
        illuminaT_++;
        break;
    case 5006092:
        rs = 121908766;
        illuminaT_++;
        break;
    case 5006103:
        rs = 78802634;
        illuminaT_++;
        break;
    case 5006112:
        rs = 75115087;
        illuminaT_++;
        break;
    case 5007145:
        rs = 137853096;
        illuminaT_++;
        break;
    case 5007146:
        rs = 137853097;
        illuminaT_++;
        break;
    case 5008215:
        rs = 76917243;
        illuminaT_++;
        break;
    case 5008436:
        rs = 137852327;
        illuminaT_++;
        break;
    case 5008440:
        rs = 137852330;
        illuminaT_++;
        break;
    case 5008441:
        rs = 267606835;
        illuminaT_++;
        break;
    case 5008450:
        rs = 137852339;
        illuminaT_++;
        break;
    case 5008462:
        rs = 137852348;
        illuminaT_++;
        break;
    case 5008753:
        rs = 193922376;
        illuminaT_++;
        break;
    case 5009095:
        rs = 397507789;
        illuminaT_++;
        break;
    case 5009097:
        rs = 397507788;
        illuminaT_++;
        break;
    case 5009099:
        rs = 397507785;
        illuminaT_++;
        break;
    case 5009107:
        rs = 397507777;
        illuminaT_++;
        break;
    case 5009119:
        rs = 397507756;
        illuminaT_++;
        break;
    case 5009120:
        rs = 397507753;
        illuminaT_++;
        break;
    case 5009136:
        rs = 397507728;
        illuminaT_++;
        break;
    case 5009151:
        rs = 276174838;
        illuminaT_++;
        break;
    case 5009161:
        rs = 397507692;
        illuminaT_++;
        break;
    case 5009162:
        rs = 886040499;
        illuminaT_++;
        break;
    case 5009163:
        rs = 397507688;
        illuminaT_++;
        break;
    case 5009165:
        rs = 397507684;
        illuminaT_++;
        break;
    case 5009173:
        rs = 80359388;
        illuminaT_++;
        break;
    case 5009174:
        rs = 397507673;
        illuminaT_++;
        break;
    case 5009175:
        rs = 397507672;
        illuminaT_++;
        break;
    case 5009179:
        rs = 397507659;
        illuminaT_++;
        break;
    case 5009215:
        rs = 397507605;
        illuminaT_++;
        break;
    case 5009223:
        rs = 397507591;
        illuminaT_++;
        break;
    case 5009244:
        rs = 397507739;
        illuminaT_++;
        break;
    case 5009256:
        rs = 1801426;
        illuminaT_++;
        break;
    case 5009299:
        rs = 11571746;
        illuminaT_++;
        break;
    case 5009331:
        rs = 55716624;
        illuminaT_++;
        break;
    case 5009334:
        rs = 169547;
        illuminaT_++;
        break;
    case 5010413:
        rs = 397507940;
        illuminaT_++;
        break;
    case 5010426:
        rs = 397507986;
        illuminaT_++;
        break;
    case 5010451:
        rs = 397507420;
        illuminaT_++;
        break;
    case 5010462:
        rs = 80359771;
        illuminaT_++;
        break;
    case 5010474:
        rs = 397507830;
        illuminaT_++;
        break;
    case 5010479:
        rs = 80359266;
        illuminaT_++;
        break;
    case 5010486:
        rs = 397507613;
        illuminaT_++;
        break;
    case 5010497:
        rs = 80359380;
        illuminaT_++;
        break;
    case 5010509:
        rs = 397507724;
        illuminaT_++;
        break;
    case 5010511:
        rs = 397507732;
        illuminaT_++;
        break;
    case 5010512:
        rs = 276174847;
        illuminaT_++;
        break;
    case 5010527:
        rs = 397507812;
        illuminaT_++;
        break;
    case 5010530:
        rs = 397507826;
        illuminaT_++;
        break;
    case 5010544:
        rs = 397507874;
        illuminaT_++;
        break;
    case 5010569:
        rs = 397507419;
        illuminaT_++;
        break;
    case 5010578:
        rs = 276174852;
        illuminaT_++;
        break;
    case 5010743:
        rs = 368505753;
        illuminaT_++;
        break;
    case 5010780:
        rs = 74467662;
        illuminaT_++;
        break;
    case 5010801:
        rs = 397508461;
        illuminaT_++;
        break;
    case 5010930:
        rs = 80282562;
        illuminaT_++;
        break;
    case 5010947:
        rs = 78440224;
        illuminaT_++;
        break;
    case 5010980:
        rs = 397508778;
        illuminaT_++;
        break;
    case 5011073:
        rs = 79031340;
        illuminaT_++;
        break;
    case 5011184:
        rs = 79031340;
        illuminaT_++;
        break;
    case 5011243:
        rs = 397508211;
        illuminaT_++;
        break;
    case 5011404:
        rs = 397508296;
        illuminaT_++;
        break;
    case 5011446:
        rs = 121908759;
        illuminaT_++;
        break;
    case 5011516:
        rs = 397508353;
        illuminaT_++;
        break;
    case 5011556:
        rs = 397515498;
        illuminaT_++;
        break;
    case 5011672:
        rs = 397508442;
        illuminaT_++;
        break;
    case 5011775:
        rs = 397508500;
        illuminaT_++;
        break;
    case 5011826:
        rs = 202179988;
        illuminaT_++;
        break;
    case 5011985:
        rs = 387906362;
        illuminaT_++;
        break;
    case 5012121:
        rs = 193922525;
        illuminaT_++;
        break;
    case 5012129:
        rs = 397508675;
        illuminaT_++;
        break;
    case 5012573:
        rs = 515726215;
        illuminaT_++;
        break;
    case 5012575:
        rs = 121908428;
        illuminaT_++;
        break;
    case 5012578:
        rs = 281865117;
        illuminaT_++;
        break;
    case 5012610:
        rs = 398124502;
        illuminaT_++;
        break;
    case 5012612:
        rs = 137852949;
        illuminaT_++;
        break;
    case 5012616:
        rs = 80338848;
        illuminaT_++;
        break;
    case 5012618:
        rs = 28939086;
        illuminaT_++;
        break;
    case 5012622:
        rs = 137852696;
        illuminaT_++;
        break;
    case 5012623:
        rs = 137852695;
        illuminaT_++;
        break;
    case 5012624:
        rs = 137852700;
        illuminaT_++;
        break;
    case 5012628:
        rs = 80356708;
        illuminaT_++;
        break;
    case 5012629:
        rs = 180177309;
        illuminaT_++;
        break;
    case 5012634:
        rs = 80338794;
        illuminaT_++;
        break;
    case 5012660:
        rs = 28937590;
        illuminaT_++;
        break;
    case 5012664:
        rs = 78340951;
        illuminaT_++;
        break;
    case 5012665:
        rs = 387906225;
        illuminaT_++;
        break;
    case 5012669:
        rs = 80356680;
        illuminaT_++;
        break;
    case 5012671:
        rs = 80356681;
        illuminaT_++;
        break;
    case 5012672:
        rs = 80356682;
        illuminaT_++;
        break;
    case 5012678:
        rs = 386833969;
        illuminaT_++;
        break;
    case 5012679:
        rs = 80338701;
        illuminaT_++;
        break;
    case 5012680:
        rs = 28936415;
        illuminaT_++;
        break;
    case 5012683:
        rs = 121918008;
        illuminaT_++;
        break;
    case 5012686:
        rs = 387906525;
        illuminaT_++;
        break;
    case 5012688:
        rs = 61750420;
        illuminaT_++;
        break;
    case 5012709:
        rs = 35887622;
        illuminaT_++;
        break;
    case 5012749:
        rs = 119466000;
        illuminaT_++;
        break;
    case 5012758:
        rs = 121434280;
        illuminaT_++;
        break;
    case 5012759:
        rs = 77931234;
        illuminaT_++;
        break;
    case 5012760:
        rs = 373715782;
        illuminaT_++;
        break;
    case 5012761:
        rs = 200724875;
        illuminaT_++;
        break;
    case 5012765:
        rs = 28940893;
        illuminaT_++;
        break;
    case 5012770:
        rs = 587776650;
        illuminaT_++;
        break;
    case 5012799:
        rs = 28941770;
        illuminaT_++;
        break;
    case 5012804:
        rs = 111033260;
        illuminaT_++;
        break;
    case 5012861:
        rs = 80338898;
        illuminaT_++;
        break;
    case 5012862:
        rs = 80338899;
        illuminaT_++;
        break;
    case 5012864:
        rs = 121965075;
        illuminaT_++;
        break;
    case 5012865:
        rs = 80338901;
        illuminaT_++;
        break;
    case 5012867:
        rs = 80338895;
        illuminaT_++;
        break;
    case 5012878:
        rs = 80356489;
        illuminaT_++;
        break;
    case 5012880:
        rs = 80356491;
        illuminaT_++;
        break;
    case 5037820:
        rs = 267608126;
        illuminaT_++;
        break;
    case 5037831:
        rs = 863225414;
        illuminaT_++;
        break;
    case 5037832:
        rs = 786201855;
        illuminaT_++;
        break;
    case 5037835:
        rs = 267608101;
        illuminaT_++;
        break;
    case 5037850:
        rs = 267608037;
        illuminaT_++;
        break;
    case 5037858:
        rs = 267608050;
        illuminaT_++;
        break;
    case 5037866:
        rs = 267608114;
        illuminaT_++;
        break;
    case 5037874:
        rs = 267608090;
        illuminaT_++;
        break;
    case 5037877:
        rs = 267608085;
        illuminaT_++;
        break;
    case 5037884:
        rs = 267608072;
        illuminaT_++;
        break;
    case 5037895:
        rs = 193922343;
        illuminaT_++;
        break;
    case 5041058:
        rs = 72658154;
        illuminaT_++;
        break;
    case 5046667:
        rs = 876660428;
        illuminaT_++;
        break;
    case 5047658:
        rs = 63750215;
        illuminaT_++;
        break;
    case 5048984:
        rs = 72551348;
        illuminaT_++;
        break;
    case 5049013:
        rs = 139607673;
        illuminaT_++;
        break;
    case 5050964:
        rs = 199474658;
        illuminaT_++;
        break;
    case 5050984:
        rs = 199474657;
        illuminaT_++;
        break;
    case 5050994:
        rs = 267606617;
        illuminaT_++;
        break;
    case 5053826:
        rs = 79031340;
        illuminaT_++;
        break;
    case 5053827:
        rs = 77409459;
        illuminaT_++;
        break;
    case 5053833:
        rs = 75115087;
        illuminaT_++;
        break;
    case 5053834:
        rs = 79633941;
        illuminaT_++;
        break;
    case 5053836:
        rs = 78194216;
        illuminaT_++;
        break;
    case 5053839:
        rs = 78802634;
        illuminaT_++;
        break;
    case 5053851:
        rs = 78440224;
        illuminaT_++;
        break;
    case 5053895:
        rs = 76151636;
        illuminaT_++;
        break;
    case 6007566:
        rs = 6151429;
        illuminaT_++;
        break;
    case 6007689:
        rs = 398123126;
        illuminaT_++;
        break;
    case 6007710:
        rs = 367543005;
        illuminaT_++;
        break;
    case 6009255:
        rs = 515726176;
        illuminaT_++;
        break;
    case 6009259:
        rs = 515726174;
        illuminaT_++;
        break;
    case 6009276:
        rs = 515726175;
        illuminaT_++;
        break;
    case 6014100:
        rs = 879254382;
        illuminaT_++;
        break;
    case 6014141:
        rs = 201573863;
        illuminaT_++;
        break;
    case 6014161:
        rs = 370471092;
        illuminaT_++;
        break;
    case 6014217:
        rs = 773658037;
        illuminaT_++;
        break;
    case 6014229:
        rs = 544453230;
        illuminaT_++;
        break;
    case 6014299:
        rs = 879254662;
        illuminaT_++;
        break;
    case 6014548:
        rs = 879255045;
        illuminaT_++;
        break;
    case 6014573:
        rs = 875989911;
        illuminaT_++;
        break;
    case 6015375:
        rs = 992677795;
        illuminaT_++;
        break;
    case 6016654:
        rs = 200511261;
        illuminaT_++;
        break;
    case 6024270:
        rs = 774159791;
        illuminaT_++;
        break;
    case 700014:
        rs = 879255033;
        illuminaT_++;
        break;
    case 700020:
        rs = 879253834;
        illuminaT_++;
        break;
    case 700076:
        rs = 767388144;
        illuminaT_++;
        break;
    case 700184:
        rs = 367543006;
        illuminaT_++;
        break;
    case 700566:
        rs = 887126161;
        illuminaT_++;
        break;
    case 700568:
        rs = 863225434;
        illuminaT_++;
        break;
    case 700621:
        rs = 1135401729;
        illuminaT_++;
        break;
    case 700645:
        rs = 781986930;
        illuminaT_++;
        break;
    case 700947:
        rs = 1085307466;
        illuminaT_++;
        break;
    case 700994:
        rs = 879254740;
        illuminaT_++;
        break;
    case 701087:
        rs = 879255213;
        illuminaT_++;
        break;
    case 701112:
        rs = 879255281;
        illuminaT_++;
        break;
    case 701164:
        rs = 879254412;
        illuminaT_++;
        break;
    case 701180:
        rs = 879254761;
        illuminaT_++;
        break;
    case 701345:
        rs = 879254817;
        illuminaT_++;
        break;
    case 701347:
        rs = 879254886;
        illuminaT_++;
        break;
    case 701362:
        rs = 879254434;
        illuminaT_++;
        break;
    case 701371:
        rs = 879254884;
        illuminaT_++;
        break;
    case 701383:
        rs = 879254443;
        illuminaT_++;
        break;
    case 701409:
        rs = 1419032418;
        illuminaT_++;
        break;
    case 701414:
        rs = 879254410;
        illuminaT_++;
        break;
    case 701450:
        rs = 879254841;
        illuminaT_++;
        break;
    case 701496:
        rs = 879255105;
        illuminaT_++;
        break;
    case 701505:
        rs = 879254521;
        illuminaT_++;
        break;
    case 701811:
        rs = 879254708;
        illuminaT_++;
        break;
    case 702110:
        rs = 879254474;
        illuminaT_++;
        break;
    case 702255:
        rs = 1461905374;
        illuminaT_++;
        break;
    case 702310:
        rs = 879254899;
        illuminaT_++;
        break;
    case 702329:
        rs = 781319410;
        illuminaT_++;
        break;
    case 702373:
        rs = 879254651;
        illuminaT_++;
        break;
    case 702455:
        rs = 879255282;
        illuminaT_++;
        break;
    case 702480:
        rs = 879254687;
        illuminaT_++;
        break;
    case 702563:
        rs = 879254404;
        illuminaT_++;
        break;
    case 702565:
        rs = 879255026;
        illuminaT_++;
        break;
    case 703107:
        rs = 879254393;
        illuminaT_++;
        break;
    case 703167:
        rs = 1553137543;
        illuminaT_++;
        break;
    case 703267:
        rs = 879254397;
        illuminaT_++;
        break;
    case 703316:
        rs = 879255311;
        illuminaT_++;
        break;
    case 703322:
        rs = 879254574;
        illuminaT_++;
        break;
    case 703359:
        rs = 879254702;
        illuminaT_++;
        break;
    case 703379:
        rs = 879255029;
        illuminaT_++;
        break;
    case 703467:
        rs = 879254673;
        illuminaT_++;
        break;
    case 703601:
        rs = 879254653;
        illuminaT_++;
        break;
    case 703652:
        rs = 879254896;
        illuminaT_++;
        break;
    case 703668:
        rs = 879254435;
        illuminaT_++;
        break;
    case 703692:
        rs = 879254614;
        illuminaT_++;
        break;
    case 703728:
        rs = 879254710;
        illuminaT_++;
        break;
    case 703733:
        rs = 879255320;
        illuminaT_++;
        break;
    case 703821:
        rs = 879254666;
        illuminaT_++;
        break;
    case 703873:
        rs = 879254923;
        illuminaT_++;
        break;
    case 703916:
        rs = 876659708;
        illuminaT_++;
        break;
    case 703960:
        rs = 879255224;
        illuminaT_++;
        break;
    case 703963:
        rs = 879254491;
        illuminaT_++;
        break;
    case 704105:
        rs = 1555803643;
        illuminaT_++;
        break;
    case 704128:
        rs = 879254436;
        illuminaT_++;
        break;
    case 704190:
        rs = 879254958;
        illuminaT_++;
        break;
    case 704225:
        rs = 879254384;
        illuminaT_++;
        break;
    case 704231:
        rs = 397515991;
        illuminaT_++;
        break;
    case 704270:
        rs = 397516073;
        illuminaT_++;
        break;
    case 704424:
        rs = 879254123;
        illuminaT_++;
        break;
    case 704512:
        rs = 879255175;
        illuminaT_++;
        break;
    case 704677:
        rs = 879254582;
        illuminaT_++;
        break;
    case 704827:
        rs = 879254573;
        illuminaT_++;
        break;
    case 704874:
        rs = 879254888;
        illuminaT_++;
        break;
    case 704887:
        rs = 879254821;
        illuminaT_++;
        break;
    case 704902:
        rs = 879254922;
        illuminaT_++;
        break;
    case 704916:
        rs = 879254552;
        illuminaT_++;
        break;
    case 704986:
        rs = 879253965;
        illuminaT_++;
        break;
    case 704992:
        rs = 879254771;
        illuminaT_++;
        break;
    case 705007:
        rs = 879254799;
        illuminaT_++;
        break;
    case 705032:
        rs = 879254569;
        illuminaT_++;
        break;
    case 705059:
        rs = 875989898;
        illuminaT_++;
        break;
    case 705119:
        rs = 879254591;
        illuminaT_++;
        break;
    case 705179:
        rs = 879254538;
        illuminaT_++;
        break;
    case 705234:
        rs = 1060499931;
        illuminaT_++;
        break;
    case 705258:
        rs = 879254413;
        illuminaT_++;
        break;
    case 705313:
        rs = 879254701;
        illuminaT_++;
        break;
    case 705428:
        rs = 879254388;
        illuminaT_++;
        break;
    case 705498:
        rs = 879254138;
        illuminaT_++;
        break;
    case 705502:
        rs = 879254885;
        illuminaT_++;
        break;
    case 705645:
        rs = 879254440;
        illuminaT_++;
        break;
    case 705657:
        rs = 879254581;
        illuminaT_++;
        break;
    case 705698:
        rs = 879254882;
        illuminaT_++;
        break;
    case 705710:
        rs = 879254594;
        illuminaT_++;
        break;
    case 705843:
        rs = 879254387;
        illuminaT_++;
        break;
    case 705867:
        rs = 879254512;
        illuminaT_++;
        break;
    case 705904:
        rs = 80357634;
        illuminaT_++;
        break;
    case 705932:
        rs = 879254402;
        illuminaT_++;
        break;
    case 706122:
        rs = 879254027;
        illuminaT_++;
        break;
    case 706178:
        rs = 879254116;
        illuminaT_++;
        break;
    case 706241:
        rs = 879254952;
        illuminaT_++;
        break;
    case 706291:
        rs = 879255031;
        illuminaT_++;
        break;
    case 706299:
        rs = 879254575;
        illuminaT_++;
        break;
    case 706312:
        rs = 879254768;
        illuminaT_++;
        break;
    case 706314:
        rs = 879254122;
        illuminaT_++;
        break;
    case 706344:
        rs = 730881471;
        illuminaT_++;
        break;
    case 706367:
        rs = 879254736;
        illuminaT_++;
        break;
    case 706371:
        rs = 879254737;
        illuminaT_++;
        break;
    case 706379:
        rs = 879254530;
        illuminaT_++;
        break;
    case 706465:
        rs = 879254748;
        illuminaT_++;
        break;
    case 706566:
        rs = 879254675;
        illuminaT_++;
        break;
    case 706617:
        rs = 879254494;
        illuminaT_++;
        break;
    case 706659:
        rs = 879254111;
        illuminaT_++;
        break;
    case 706716:
        rs = 879254980;
        illuminaT_++;
        break;
    case 706888:
        rs = 879254580;
        illuminaT_++;
        break;
    case 709033:
        rs = 864622557;
        illuminaT_++;
        break;
    case 709034:
        rs = 864622558;
        illuminaT_++;
        break;
    case 709063:
        rs = 80359264;
        illuminaT_++;
        break;
    case 709064:
        rs = 864622609;
        illuminaT_++;
        break;
    case 709068:
        rs = 864622073;
        illuminaT_++;
        break;
    case 709069:
        rs = 864622082;
        illuminaT_++;
        break;
    case 709070:
        rs = 864622200;
        illuminaT_++;
        break;
    case 709076:
        rs = 864622277;
        illuminaT_++;
        break;
    case 709466:
        rs = 150074056;
        illuminaT_++;
        break;
    case 712972:
        rs = 864622651;
        illuminaT_++;
        break;
    case 723120:
        rs = 864622480;
        illuminaT_++;
        break;
    case 723181:
        rs = 864622257;
        illuminaT_++;
        break;
    case 723189:
        rs = 864622161;
        illuminaT_++;
        break;
    case 723191:
        rs = 864622431;
        illuminaT_++;
        break;
    case 723194:
        rs = 864622509;
        illuminaT_++;
        break;
    case 723202:
        rs = 864622192;
        illuminaT_++;
        break;
    case 723205:
        rs = 864622481;
        illuminaT_++;
        break;
    case 723234:
        rs = 864622707;
        illuminaT_++;
        break;

    default:illuminaU_++; //untranslaned lines
        break;
    }
    return rs;
}