float result;

float p;

float p2;

friend class Multi_Seq_Obj;

Seq_Obj(string &_ID, unsigned int _Pos, string &_Ref, int _Num_Two,

string &_Ref_Info, string &_Seq, string &_Seq_Two, unsigned int type, float step, float end)

{

this->ID = _ID;

this->Pos = _Pos;

this->Ref = _Ref;

this->Num_Two = _Num_Two;

this->Ref_Info = _Ref_Info;

this->Seq_Qual_1 = _Seq;

this->Seq_Qual_2 = _Seq_Two;

this->Type = type;

initVectors(type, step, end);

this->Max_allele = 'N';

this->Max_allele_count = 0;

}

Seq_Obj()

{

this->ID = "";

this->Pos = 0;

this->Ref = "";

this->Num_Two = -1;

this->Ref_Info = "";

this->Seq_Qual_1 = "";

this->Seq_Qual_2 = "";

this->Type = 0;

this->Max_allele = 'N';

this->Max_allele_count = 0;

}

Seq_Obj(vector<string> &obj, unsigned int type, float step, float end)

{

this->ID = obj[0];

this->Pos = stoi(obj[1]);

this->Ref = obj[2];

this->Num_Two = stoi(obj[3]);

this->Ref_Info = obj[4];

this->Seq_Qual_1 = obj[5];

this->Seq_Qual_2 = obj[6];

this->Type = type;

initVectors(type, step, end);

this->Max_allele = 'N';

this->Max_allele_count = 0;

}

Seq_Obj(array<string, 7> &obj, unsigned int type, float step, float end)

{

this->ID = obj[0];

this->Pos = stoi(obj[1]);

this->Ref = obj[2];

this->Num_Two = stoi(obj[3]);

this->Ref_Info = obj[4];

this->Seq_Qual_1 = obj[5];

this->Seq_Qual_2 = obj[6];

this->Type = type;

initVectors(type, step, end);

this->Max_allele = 'N';

this->Max_allele_count = 0;

}

inline int Get_Max_Allele_Count()

{

return this->Max_allele_count;

}

inline char Get_Max_Allele()

{

return this->Max_allele;

}

inline string Get_ID()

{

return this->ID;

}

inline unsigned int Get_Pos()

{

return this->Pos;

}

inline int Get_Ref_Length()

{

return Ref_Info.size();

}

inline string Get_Ref()

{

return this->Ref;

}

inline string Get_Ref_Info()

{

return this->Ref_Info;

}

inline string Get_Seq_Qual(int n)

{

return (n == 0) ? this->Seq_Qual_1 : this->Seq_Qual_2;

}

inline float Get_Value_Result(const unsigned int n)

{

if (this->Value.empty())

{

cerr << "No value\t" << ID << endl;

return 0.0;

}

if (this->Value.size() <= n)

{

cerr << "out of range\t" << ID << endl;

return 0.0;

}

return this->Value[n].result;

}

inline float Get_Value_P(const unsigned int n, const int i)

{

if (this->Value.empty())

{

cerr << "No value\t" << ID << endl;

return 0.0;

}

if (this->Value.size() <= n)

{

cerr << "out of range\t" << ID << endl;

return 0.0;

}

if (i == 0)

return this->Value[n].p;

else

return this->Value[n].p2;

}

inline vector<int> getClassCounter()

{

return this->classCounter;

}

inline vector<float> getValuesVector()

{

return this->valuesVector;

}

int Seq_Init_Filter();

int Seq_Qual_Filter(int bq, int mq);

int Seq_Max_Filter(const unsigned int max_count);

float Get_Ratio_nchar();

float Get_Ratio_del();

void Calc_W();

int Calc_Value(float end, float step);float Calc_Value(float test_p, float test_p_2, int type);

float Get_Value_Result_Max();

int Get_Value_Result_Max_Index();

void pre_Calc_Value();

float get_Calc_Value(float step0, float step1, int type, float step_length);

int Num_Two;

unsigned int Type;

unsigned int Pos;

string ID;

string Ref;

string Ref_Info;

string Seq_Qual_1;

string Seq_Qual_2;

vector<float> W;

vector<internal_value> Value;

char Max_allele;

int Max_allele_count;

vector<int> classCounter;

vector<float> valuesVector;

//To save the Calc_Values

vector<float> typeoneVec;

vector<float> typetwoVec;

vector<float> typethreeVec;

float step;

float end;

inline void initVectors(int type, float step, float end)

{

this->step = step;

this->end = end;

this->classCounter.resize(4, 0);

this->valuesVector.resize(3 * type, 0.0);

this->W.resize(this->Ref_Info.size(), 0.0);

this->Value.resize(type);

this->typeoneVec.resize(floor((end - step / 10) / step));

this->typetwoVec.resize(floor((end - step / 10) / step));

this->typethreeVec.resize(floor((end - step / 10) / step) * floor((end - step / 10) / step));

}

{

func_ptr[0][0] = func_1;

func_ptr[0][1] = func_2;

func_ptr[1][0] = func_2;

func_ptr[1][1] = func_1;

func_ptr[2][0] = func_3;

func_ptr[2][1] = func_4;

return 0;