void read_ancestrymap (char* input_file, int N, int M, int* data)
{
FILE *File = NULL;
int i, j, allele;
char tmp[512] = "";
char ref[512] = "";
int max_char_per_line = 1000;
char szbuff[max_char_per_line];
int warning = 0;
// open input file
File = fopen_read(input_file);
j = 0;
i = 0;
// while not the end of the file
// or not too many SNPs (j < M-1)
// or last SNP but not too many ind (j == (M-1) && i< N))
while (fgets(szbuff,max_char_per_line, File) && (j < M-1 || (j == (M-1) && i< N))) {
// read line
read_line_ancestrymap(szbuff, &allele, tmp, i+1, j+1, input_file, &warning);
// first SNP, save SNP name
if (j == 0 && i == 0)
strcpy(ref, tmp);
// new SNP
if (strcmp(ref, tmp) != 0) {
// test if the number indiviual for the line is ok
test_column (input_file, File, i, j+1, N, NULL);
// new line
i = 0;
j++;
// save new SNP name
strcpy(ref, tmp);
}
// write genotype
data[i * M + j] = allele;
i++;
}
test_column (input_file, File, i, j+1, N, NULL);
// test the number of lines
test_line(input_file, File, j+1, M);
fclose(File);
}
int main (int argc, char *argv[])
{
// parameters
int i1, i2, N;
char *token = NULL;
FILE *m_File;
// command line args configuration
i1 = (int) atoi(argv[1]);
i2 = (int) atoi(argv[2]);
N = (int) atoi(argv[3]);
if (argc > 4) {
token = (char *) calloc(4, sizeof(char));
token = "tmp";
}
// test test_column
m_File = fopen("files/test.txt","r");
test_column("files/test.txt",m_File, i1, 10, N, token);
// test test_line
test_line("files/test.txt", m_File, i2, N);
return 0;
}
void read_data_int(char *file_data, int N, int M, int *dat)
{
FILE *m_File = NULL;
int i = 0;
int j = 0;
int max_char_per_line = MAX_LENGTH_NB_INT * M + 20;
char *szbuff;
char *token;
// allocate memory
szbuff = (char *) malloc(max_char_per_line * sizeof(char));
// open file
m_File = fopen_read(file_data);
i = 0;
while (fgets(szbuff, max_char_per_line, m_File) && (i < N)) {
j = 0;
// cut line with split character SEP (" ")
token = strtok(szbuff, SEP);
// read elements and register them in dat
while (token && j < M) {
//printf("%s\n",token);
dat[i * M + j] = (int)atof(token);
// next elements
token = strtok(NULL, SEP);
j++;
}
i++;
// check the number of columns
test_column(file_data, m_File, j, i, M, token);
}
// check the number of lines
test_line(file_data, m_File, i, N);
// close file
fclose(m_File);
// free memory
free(szbuff);
}
