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-rw-r--r--src/io.cpp106
1 files changed, 59 insertions, 47 deletions
diff --git a/src/io.cpp b/src/io.cpp
index 941bacf..923eb11 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -216,8 +216,9 @@ bool ReadFile_log(const string &file_log, double &pheno_mean) {
char *ch_ptr;
size_t flag = 0;
+ auto infilen = file_log.c_str();
while (getline(infile, line)) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
ch_ptr = strtok(NULL, " , \t");
if (ch_ptr != NULL && strcmp(ch_ptr, "estimated") == 0) {
@@ -225,7 +226,7 @@ bool ReadFile_log(const string &file_log, double &pheno_mean) {
if (ch_ptr != NULL && strcmp(ch_ptr, "mean") == 0) {
ch_ptr = strtok(NULL, " , \t");
if (ch_ptr != NULL && strcmp(ch_ptr, "=") == 0) {
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
pheno_mean = atof(ch_ptr);
flag = 1;
}
@@ -322,8 +323,9 @@ bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
string id;
double p;
+ auto infilen = file_pheno.c_str();
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
for (int i = 0; i < (p_column - 1); ++i) {
ch_ptr = strtok(NULL, " , \t");
}
@@ -494,18 +496,19 @@ bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo) {
string major;
string minor;
+ auto infilen = file_bim.c_str();
while (getline(infile, line)) {
- ch_ptr = strtok_safe((char *)line.c_str(), " \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " \t",infilen);
chr = ch_ptr;
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
rs = ch_ptr;
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
cM = atof(ch_ptr);
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
b_pos = atol(ch_ptr);
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
minor = ch_ptr;
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
major = ch_ptr;
SNPINFO sInfo = {chr, rs, cM, b_pos, minor, major, 0, -9, -9, 0, 0, 0};
@@ -550,14 +553,15 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
ind_pheno_row.push_back(0);
}
+ auto infilen = file_fam.c_str();
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok_safe((char *)line.c_str(), " \t");
- ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
id = ch_ptr;
- ch_ptr = strtok_safe(NULL, " \t");
- ch_ptr = strtok_safe(NULL, " \t");
- ch_ptr = strtok_safe(NULL, " \t");
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " \t",infilen);
size_t i = 0;
while (i < p_max) {
@@ -657,12 +661,13 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
file_pos = 0;
auto count_warnings = 0;
+ auto infilen = file_geno.c_str();
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
rs = ch_ptr;
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
minor = ch_ptr;
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
major = ch_ptr;
if (setSnps.size() != 0 && setSnps.count(rs) == 0) {
@@ -702,8 +707,9 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
n_2 = 0;
c_idv = 0;
gsl_vector_set_zero(genotype_miss);
+ auto infilen = file_geno.c_str();
for (int i = 0; i < ni_total; ++i) {
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
if (indicator_idv[i] == 0)
continue;
@@ -1193,12 +1199,13 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
double Cov_d;
size_t n_id1, n_id2;
+ auto infilen=file_kin.c_str();
while (getline(infile, line)) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
id1 = ch_ptr;
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
id2 = ch_ptr;
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
d = atof(ch_ptr);
if (mapID2num.count(id1) == 0 || mapID2num.count(id2) == 0) {
continue;
@@ -1330,7 +1337,7 @@ void ReadFile_eigenD(const string &file_kd, bool &error, gsl_vector *eval) {
error = true;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_kd.c_str());
d = atof(ch_ptr);
ch_ptr = strtok(NULL, " , \t");
@@ -1667,22 +1674,23 @@ bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
int c_idv = 0, c_snp = 0;
+ auto infilen = file_geno.c_str();
for (int i = 0; i < ns_total; ++i) {
safeGetline(infile, line).eof();
if (indicator_snp[i] == 0) {
continue;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
c_idv = 0;
geno_mean = 0;
n_miss = 0;
gsl_vector_set_zero(genotype_miss);
for (int j = 0; j < ni_total; ++j) {
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
if (indicator_idv[j] == 0) {
continue;
}
@@ -1776,22 +1784,23 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
size_t c_idv = 0, c_snp = 0;
+ auto infilen = file_geno.c_str();
for (size_t i = 0; i < ns_total; ++i) {
safeGetline(infile, line).eof();
if (indicator_snp[i] == 0) {
continue;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
c_idv = 0;
geno_mean = 0;
n_miss = 0;
gsl_vector_set_zero(genotype_miss);
for (uint j = 0; j < ni_total; ++j) {
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
if (indicator_idv[j] == 0) {
continue;
}
@@ -2140,8 +2149,9 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
size_t n = *max_element(est_column.begin(), est_column.end());
+ auto infilen = file_est.c_str();
while (getline(infile, line)) {
- ch_ptr = strtok_safe((char *)line.c_str(), " \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " \t",infilen);
alpha = 0.0;
beta = 0.0;
@@ -2222,7 +2232,7 @@ bool ReadFile_gene(const string &file_gene, vector<double> &vec_read,
getline(infile, line);
while (getline(infile, line)) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_gene.c_str());
rs = ch_ptr;
ch_ptr = strtok(NULL, " , \t");
@@ -2572,7 +2582,7 @@ bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
// Read the following lines to record mapRS2cat.
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_cat.c_str());
i_cat = 0;
for (size_t i = 0; i < header.coln; i++) {
@@ -2704,9 +2714,10 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
if (indicator_snp[t] == 0)
continue;
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
- ch_ptr = strtok_safe(NULL, " , \t");
+ auto infilen = file_geno.c_str();
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
rs = snpInfo[t].rs_number; // This line is new.
@@ -2720,7 +2731,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
if (indicator_idv[i] == 0) {
continue;
}
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
if (strcmp(ch_ptr, "NA") == 0) {
gsl_vector_set(geno_miss, i, 0);
n_miss++;
@@ -3161,10 +3172,11 @@ bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2weight) {
string line, rs;
double weight;
+ auto infilen = file_wsnp.c_str();
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
rs = ch_ptr;
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
weight = atof(ch_ptr);
mapRS2weight[rs] = weight;
}
@@ -3200,7 +3212,7 @@ bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_wcat.c_str());
size_t t = 0;
for (size_t i = 0; i < header.coln; i++) {
@@ -3307,7 +3319,7 @@ void ReadFile_beta(const string &file_beta,
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_beta.c_str());
z = 0;
beta = 0;
@@ -3489,7 +3501,7 @@ void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_beta.c_str());
z = 0;
beta = 0;
@@ -3777,7 +3789,7 @@ void ReadFile_vector(const string &file_vec, gsl_vector *vec) {
for (size_t i = 0; i < vec->size; i++) {
safeGetline(infile, line).eof();
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_vec.c_str());
gsl_vector_set(vec, i, atof(ch_ptr));
}
@@ -3800,7 +3812,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat) {
for (size_t i = 0; i < mat->size1; i++) {
safeGetline(infile, line).eof();
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_mat.c_str());
for (size_t j = 0; j < mat->size2; j++) {
enforce(ch_ptr);
gsl_matrix_set(mat, i, j, atof(ch_ptr));
@@ -3828,7 +3840,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1,
for (size_t i = 0; i < mat1->size1; i++) {
safeGetline(infile, line).eof();
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_mat.c_str());
for (size_t j = 0; j < mat1->size2; j++) {
enforce(ch_ptr);
gsl_matrix_set(mat1, i, j, atof(ch_ptr));
@@ -3838,7 +3850,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1,
for (size_t i = 0; i < mat2->size1; i++) {
safeGetline(infile, line).eof();
- ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",file_mat.c_str());
for (size_t j = 0; j < mat2->size2; j++) {
enforce(ch_ptr);
gsl_matrix_set(mat2, i, j, atof(ch_ptr));
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 02:32:38 +0000