int main(int argc, char *argv[] )
{
//========= WORK WITH R INTERFACE ===========
int Total_Num_SNPSets;
int Total_Num_SNP;
int Total_Num_IND;
int my_error;
/*
Generate_MWA_SetID_File((char*)"../data/Example1.bed",(char*)"../data/Example1.bim",(char*)"../data/Example1.fam",
(char*)"../data/Example1.SetID", (char*)"../data/Example1_0124_SetID.mwa", (char*)"../data/Example1_0124_INFO.txt",&my_error);
*/
/*
Generate_MWA_SetID_File((char*)"../data/reiner.bed",(char*)"../data/reiner.bim",(char*)"../data/reiner.fam",
(char*)"../data/reiner.SetID", (char*)"../data/reiner_0124_SetID.mwa", (char*)"../data/reiner_0124_INFO.txt",&my_error);
if(my_error != 0)
return 0;
Kill_MWA_SetID_File();
*/
/* Open_MWA((char*)"../data/reiner_0124_SetID.mwa", (char*)"../data/reiner_0124_INFO.txt",&my_error); */
Open_MWA((char*)"/home/seunggeun/Project/Kernel_Machine/Test_From_Others/Yasin/test.SSD"
, (char*)"/home/seunggeun/Project/Kernel_Machine/Test_From_Others/Yasin/test.SSD.info",&my_error);
if(my_error != 0)
return 0;
Get_TotalNumberofSets(&Total_Num_SNPSets);
Get_TotalNumberofSNPs(&Total_Num_SNP);
Get_TotalNumberofInd( &Total_Num_IND);
int Num_SNP7;
int* TheGenotypesArray7;
int size;
int i;
for (i = 1; i < Total_Num_SNPSets+1; ++ i)
{
Get_NumberofSnps(i,&Num_SNP7, &my_error);
if(my_error != 0) continue;
TheGenotypesArray7 = new int [Total_Num_IND*Num_SNP7];
size = Total_Num_IND*Num_SNP7;
Get_Genotypes(i, TheGenotypesArray7,size, 1,&my_error); // int Is_MakeFile = 1 -> print set to file, 0 -> don't
Get_Genotypes(i, TheGenotypesArray7,size, 1,&my_error);
//delete [] TheGenotypesArray7;
if(my_error != 0) continue;
}
/*
Get_NumberofSnps(1,&Num_SNP7, &my_error);
//if(my_error != 0) continue;
TheGenotypesArray7 = new int [Total_Num_IND*Num_SNP7];
size = Total_Num_IND*Num_SNP7;
Get_Genotypes(1, TheGenotypesArray7,size, 1,&my_error); // int Is_MakeFile = 1 -> print set to file, 0 -> don't
delete [] TheGenotypesArray7;
//if(my_error != 0) continue;
for (i = 1; i < 11; ++ i)
{
Get_NumberofSnps(i,&Num_SNP7, &my_error);
if(my_error != 0) continue;
TheGenotypesArray7 = new int [Total_Num_IND*Num_SNP7];
size = Total_Num_IND*Num_SNP7;
Get_Genotypes(i, TheGenotypesArray7,size, 1,&my_error); // int Is_MakeFile = 1 -> print set to file, 0 -> don't
delete [] TheGenotypesArray7;
if(my_error != 0) continue;
}
*/
Close_MWA();
return 1;
//============================================================
Generate_MWA_MovingWindow( (char*)"../data/CEU.bed",(char*)"../data/CEU.bim",(char*)"../data/CEU.fam",
(char*)"../data/CEU_MW.mwa", 20, 5, (char*)"../data/MW_INFO.txt",&my_error );
Kill_MWA_MovingWindow();
Open_MWA((char*)"../data/CEU_MW.mwa",(char*)"../data/MW_INFO.txt",&my_error);
Get_TotalNumberofSets(&Total_Num_SNPSets);
Get_TotalNumberofSNPs(&Total_Num_SNP);
Get_TotalNumberofInd( &Total_Num_IND);
int Num_SNP25;
Get_NumberofSnps(25,&Num_SNP25,&my_error);
int* TheGenotypesArray25 = new int [Total_Num_IND*Num_SNP25];
Get_Genotypes(25, TheGenotypesArray25,Total_Num_IND*Num_SNP25, 1,&my_error);
Close_MWA();
//============================================================
//Generate_MWA_SetID_File((char*)"../data/CEU.bed",(char*)"../data/CEU.bim",(char*)"../data/CEU.fam"
// , (char*)"../data/SetID.TXT", (char*)"../data/CEU_SetID.mwa", (char*)"../data/SetID_INFO.txt",&my_error);
//if(my_error != 0) return 0;
//Kill_MWA_SetID_File();
/*
Open_MWA((char*)"../data/CEU_SetID.mwa", (char*)"../data/SetID_INFO.txt",&my_error);
if(my_error != 0) return 0;
Get_TotalNumberofSets(&Total_Num_SNPSets);
Get_TotalNumberofSNPs(&Total_Num_SNP);
Get_TotalNumberofInd( &Total_Num_IND);
int Num_SNP8;
int* TheGenotypesArray8;
for (int i = 1; i < 9; ++i)
{
Get_NumberofSnps(i,&Num_SNP8, &my_error);
if(my_error != 0) continue;
TheGenotypesArray8 = new int[Total_Num_IND*Num_SNP8];
int size = 5; //Total_Num_IND*Num_SNP8;
Get_Genotypes(i, TheGenotypesArray8,size, 1,&my_error); // int Is_MakeFile = 1 -> print set to file, 0 -> don't
delete [] TheGenotypesArray8;
if(my_error != 0) continue;
}
Close_MWA();
*/
//============================================
//Generate_MWA_MovingWindow( (char*)"../data/CEU.bed",(char*)"../data/CEU.bim",(char*)"../data/CEU.fam",
// (char*)"../data/CEU_MW.mwa", 20, 5, (char*)"../data/MW_INFO.txt",&my_error );
Open_MWA((char*)"../data/CEU_MW.mwa",(char*)"../data/MW_INFO.txt",&my_error);
Get_TotalNumberofSets(&Total_Num_SNPSets);
Get_TotalNumberofSNPs(&Total_Num_SNP);
Get_TotalNumberofInd( &Total_Num_IND);
int Num_SNP9;
Get_NumberofSnps(4,&Num_SNP9,&my_error);
int* TheGenotypesArray9 = new int [Total_Num_IND*Num_SNP9];
Get_Genotypes(4, TheGenotypesArray9,Total_Num_IND*Num_SNP9, 1,&my_error);
Close_MWA();
//Kill_MWA_MovingWindow();
/*
//int* TheGenotypesArray = NULL;
//Get_Genotypes(-33, TheGenotypesArray);
//Get_Genotypes(33, TheGenotypesArray);
//Get_Genotypes(51, TheGenotypesArray);
//Get_Genotypes(30, TheGenotypesArray);
int Num_SNP1, Num_SNP2, Num_SNP3,Num_SNP4,Num_SNP5;
Get_NumberofSnps(33,&Num_SNP1);
Get_NumberofSnps(-14,&Num_SNP2);
Get_NumberofSnps(5000,&Num_SNP3);
Get_NumberofSnps(2,&Num_SNP4);
Get_NumberofSnps(1,&Num_SNP5);
*/
//========= END OF WORK WITH R INTERFACE ===========
//======================================================================================================
//SBM = SETID BEDFILE MERGE
/* Hasht hash_table("../data/SetID.TXT", "../data/CEU.bim");
BedFileReader bed_pedigree( "../data/CEU.bed","../data/CEU.bim","../data/CEU.fam","../data/CEU.mwa",&hash_table);
MwoFileReader mwa("../data/CEU.mwa", NULL, &bed_pedigree); //it will take also "CEU.bed.INFO.txt"
mwa.get_set(1); //some integer - enter the value base on CEU.bed.INFO.txt
mwa.get_set(2); //some integer - enter the value base on CEU.bed.INFO.txt
mwa.get_set(3); //some integer - enter the value base on CEU.bed.INFO.txt
*/
// int a;
// mwa.get_TotalNumberofSets(&a);
//
}
void R_Get_Genotypes( int *Set_number, int * Z , int * size, int *Is_MakeFile, int * err) // set_number base on INFO file. The result will be printed to file.
{
Get_Genotypes( *Set_number, Z, *size, * Is_MakeFile, err);
}
