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-rw-r--r--src/io.cpp160
1 files changed, 79 insertions, 81 deletions
diff --git a/src/io.cpp b/src/io.cpp
index 8abdeec..35a59ee 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -152,7 +152,7 @@ bool ReadFile_snps_header(const string &file_snps, set<string> &setSnps) {
// Read header.
HEADER header;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
ReadHeader_io(line, header);
if (header.rs_col == 0 && (header.chr_col == 0 || header.pos_col == 0)) {
@@ -208,7 +208,7 @@ bool ReadFile_log(const string &file_log, double &pheno_mean) {
size_t flag = 0;
while (getline(infile, line)) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
ch_ptr = strtok(NULL, " , \t");
if (ch_ptr != NULL && strcmp(ch_ptr, "estimated") == 0) {
@@ -216,7 +216,7 @@ 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(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
pheno_mean = atof(ch_ptr);
flag = 1;
}
@@ -314,7 +314,7 @@ bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
string id;
double p;
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
for (int i = 0; i < (p_column - 1); ++i) {
ch_ptr = strtok(NULL, " , \t");
}
@@ -486,17 +486,17 @@ bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo) {
string minor;
while (getline(infile, line)) {
- ch_ptr = strtok((char *)line.c_str(), " \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " \t");
chr = ch_ptr;
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
rs = ch_ptr;
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
cM = atof(ch_ptr);
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
b_pos = atol(ch_ptr);
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
minor = ch_ptr;
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
major = ch_ptr;
SNPINFO sInfo = {chr, rs, cM, b_pos, minor, major, 0, -9, -9, 0, 0, 0};
@@ -542,12 +542,12 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
}
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok((char *)line.c_str(), " \t");
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
id = ch_ptr;
- ch_ptr = strtok(NULL, " \t");
- ch_ptr = strtok(NULL, " \t");
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
ch_ptr = strtok(NULL, " \t");
size_t i = 0;
@@ -649,11 +649,11 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
file_pos = 0;
auto count_warnings = 0;
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
rs = ch_ptr;
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
minor = ch_ptr;
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
major = ch_ptr;
if (setSnps.size() != 0 && setSnps.count(rs) == 0) {
@@ -694,7 +694,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
c_idv = 0;
gsl_vector_set_zero(genotype_miss);
for (int i = 0; i < ni_total; ++i) {
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
if (indicator_idv[i] == 0)
continue;
@@ -1004,13 +1004,13 @@ bool Bimbam_ReadOneSNP(const size_t inc, const vector<int> &indicator_idv,
bool flag = false;
for (size_t i = 0; i < inc; i++) {
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
}
if (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
- ch_ptr = strtok(NULL, " , \t");
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
geno_mean = 0.0;
double d;
@@ -1018,7 +1018,7 @@ bool Bimbam_ReadOneSNP(const size_t inc, const vector<int> &indicator_idv,
vector<size_t> geno_miss;
for (size_t i = 0; i < ni_total; ++i) {
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
if (indicator_idv[i] == 0) {
continue;
}
@@ -1134,9 +1134,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
size_t i_test = 0, i_total = 0, j_test = 0, j_total = 0;
while (getline(infile, line)) {
if (i_total == ni_total) {
- cout << "error! number of rows in the kinship "
- << "file is larger than the number of phentypes." << endl;
- error = true;
+ fail_msg("number of rows in the kinship file is larger than the number of phentypes");
}
if (indicator_idv[i_total] == 0) {
@@ -1149,10 +1147,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
ch_ptr = strtok((char *)line.c_str(), " , \t");
while (ch_ptr != NULL) {
if (j_total == ni_total) {
- cout << "error! number of columns in the "
- << "kinship file is larger than the number"
- << " of phenotypes for row = " << i_total << endl;
- error = true;
+ fail_msg(string("number of columns in the kinship file is larger than the number of individuals for row = ")+to_string(i_total));
}
d = atof(ch_ptr);
@@ -1165,18 +1160,14 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
ch_ptr = strtok(NULL, " , \t");
}
if (j_total != ni_total) {
- cout << "error! number of columns in the kinship "
- << "file do not match the number of phentypes for "
- << "row = " << i_total << endl;
- error = true;
+ string msg = "number of columns in the kinship file does not match the number of individuals for row = " + to_string( i_total );
+ fail_msg(msg);
}
i_total++;
i_test++;
}
if (i_total != ni_total) {
- cout << "error! number of rows in the kinship file do "
- << "not match the number of phenotypes." << endl;
- error = true;
+ fail_msg("number of rows in the kinship file does not match the number of individuals.");
}
} else {
map<size_t, size_t> mapID2ID;
@@ -1193,11 +1184,11 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
size_t n_id1, n_id2;
while (getline(infile, line)) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
id1 = ch_ptr;
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
id2 = ch_ptr;
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
d = atof(ch_ptr);
if (mapID2num.count(id1) == 0 || mapID2num.count(id2) == 0) {
continue;
@@ -1212,9 +1203,10 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
Cov_d = gsl_matrix_get(G, n_id1, n_id2);
if (Cov_d != 0 && Cov_d != d) {
- cout << "error! redundant and unequal terms in the "
+ cerr << "error! redundant and unequal terms in the "
<< "kinship file, for id1 = " << id1 << " and id2 = " << id2
<< endl;
+ fail_msg("");
} else {
gsl_matrix_set(G, n_id1, n_id2, d);
gsl_matrix_set(G, n_id2, n_id1, d);
@@ -1253,7 +1245,6 @@ void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv,
infile.close();
infile.clear();
- return;
}
void ReadFile_eigenU(const string &file_ku, bool &error, gsl_matrix *U) {
@@ -1329,7 +1320,7 @@ void ReadFile_eigenD(const string &file_kd, bool &error, gsl_vector *eval) {
error = true;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
d = atof(ch_ptr);
ch_ptr = strtok(NULL, " , \t");
@@ -1380,7 +1371,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps,
size_t ns_test = 0;
for (size_t t = 0; t < indicator_snp.size(); ++t) {
string line;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
@@ -1662,21 +1653,21 @@ bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
int c_idv = 0, c_snp = 0;
for (int i = 0; i < ns_total; ++i) {
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
if (indicator_snp[i] == 0) {
continue;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
- ch_ptr = strtok(NULL, " , \t");
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
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(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
if (indicator_idv[j] == 0) {
continue;
}
@@ -1771,21 +1762,21 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
size_t c_idv = 0, c_snp = 0;
for (size_t i = 0; i < ns_total; ++i) {
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
if (indicator_snp[i] == 0) {
continue;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
- ch_ptr = strtok(NULL, " , \t");
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
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(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
if (indicator_idv[j] == 0) {
continue;
}
@@ -2135,7 +2126,7 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
size_t n = *max_element(est_column.begin(), est_column.end());
while (getline(infile, line)) {
- ch_ptr = strtok((char *)line.c_str(), " \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " \t");
alpha = 0.0;
beta = 0.0;
@@ -2154,7 +2145,7 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
gamma = atof(ch_ptr);
}
if (i < n) {
- ch_ptr = strtok(NULL, " \t");
+ ch_ptr = strtok_safe(NULL, " \t");
}
}
@@ -2212,7 +2203,7 @@ bool ReadFile_gene(const string &file_gene, vector<double> &vec_read,
getline(infile, line);
while (getline(infile, line)) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
rs = ch_ptr;
ch_ptr = strtok(NULL, " , \t");
@@ -2536,7 +2527,7 @@ bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
// Read header.
HEADER header;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
ReadHeader_io(line, header);
// Use the header to count the number of categories.
@@ -2562,10 +2553,11 @@ 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((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
i_cat = 0;
for (size_t i = 0; i < header.coln; i++) {
+ enforce(ch_ptr);
if (header.rs_col != 0 && header.rs_col == i + 1) {
rs = ch_ptr;
} else if (header.chr_col != 0 && header.chr_col == i + 1) {
@@ -2686,16 +2678,16 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
size_t ns_test = 0;
for (size_t t = 0; t < indicator_snp.size(); ++t) {
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
ProgressBar("Reading SNPs", t, indicator_snp.size() - 1);
}
if (indicator_snp[t] == 0)
continue;
- ch_ptr = strtok((char *)line.c_str(), " , \t");
- ch_ptr = strtok(NULL, " , \t");
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
rs = snpInfo[t].rs_number; // This line is new.
@@ -2709,7 +2701,7 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
if (indicator_idv[i] == 0) {
continue;
}
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
if (strcmp(ch_ptr, "NA") == 0) {
gsl_vector_set(geno_miss, i, 0);
n_miss++;
@@ -3151,9 +3143,9 @@ bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2weight) {
double weight;
while (!safeGetline(infile, line).eof()) {
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
rs = ch_ptr;
- ch_ptr = strtok(NULL, " , \t");
+ ch_ptr = strtok_safe(NULL, " , \t");
weight = atof(ch_ptr);
mapRS2weight[rs] = weight;
}
@@ -3182,17 +3174,18 @@ bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
// Read header.
HEADER header;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
ReadHeader_io(line, header);
while (!safeGetline(infile, line).eof()) {
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
size_t t = 0;
for (size_t i = 0; i < header.coln; i++) {
+ enforce(ch_ptr);
if (header.rs_col != 0 && header.rs_col == i + 1) {
rs = ch_ptr;
} else if (header.chr_col != 0 && header.chr_col == i + 1) {
@@ -3274,7 +3267,7 @@ void ReadFile_beta(const string &file_beta,
// Read header.
HEADER header;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
ReadHeader_io(line, header);
if (header.n_col == 0) {
@@ -3296,7 +3289,7 @@ void ReadFile_beta(const string &file_beta,
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
z = 0;
beta = 0;
@@ -3311,6 +3304,7 @@ void ReadFile_beta(const string &file_beta,
af = 0;
var_x = 0;
for (size_t i = 0; i < header.coln; i++) {
+ enforce(ch_ptr);
if (header.rs_col != 0 && header.rs_col == i + 1) {
rs = ch_ptr;
}
@@ -3456,7 +3450,7 @@ void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
// Read header.
HEADER header;
- !safeGetline(infile, line).eof();
+ safeGetline(infile, line).eof();
ReadHeader_io(line, header);
if (header.n_col == 0) {
@@ -3477,7 +3471,7 @@ void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
if (isBlankLine(line)) {
continue;
}
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
z = 0;
beta = 0;
@@ -3492,6 +3486,7 @@ void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
af = 0;
var_x = 0;
for (size_t i = 0; i < header.coln; i++) {
+ enforce(ch_ptr);
if (header.rs_col != 0 && header.rs_col == i + 1) {
rs = ch_ptr;
}
@@ -3762,8 +3757,8 @@ void ReadFile_vector(const string &file_vec, gsl_vector *vec) {
char *ch_ptr;
for (size_t i = 0; i < vec->size; i++) {
- !safeGetline(infile, line).eof();
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ safeGetline(infile, line).eof();
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
gsl_vector_set(vec, i, atof(ch_ptr));
}
@@ -3785,9 +3780,10 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat) {
char *ch_ptr;
for (size_t i = 0; i < mat->size1; i++) {
- !safeGetline(infile, line).eof();
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ safeGetline(infile, line).eof();
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
for (size_t j = 0; j < mat->size2; j++) {
+ enforce(ch_ptr);
gsl_matrix_set(mat, i, j, atof(ch_ptr));
ch_ptr = strtok(NULL, " , \t");
}
@@ -3812,18 +3808,20 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1,
char *ch_ptr;
for (size_t i = 0; i < mat1->size1; i++) {
- !safeGetline(infile, line).eof();
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ safeGetline(infile, line).eof();
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
for (size_t j = 0; j < mat1->size2; j++) {
+ enforce(ch_ptr);
gsl_matrix_set(mat1, i, j, atof(ch_ptr));
ch_ptr = strtok(NULL, " , \t");
}
}
for (size_t i = 0; i < mat2->size1; i++) {
- !safeGetline(infile, line).eof();
- ch_ptr = strtok((char *)line.c_str(), " , \t");
+ safeGetline(infile, line).eof();
+ ch_ptr = strtok_safe((char *)line.c_str(), " , \t");
for (size_t j = 0; j < mat2->size2; j++) {
+ enforce(ch_ptr);
gsl_matrix_set(mat2, i, j, atof(ch_ptr));
ch_ptr = strtok(NULL, " , \t");
}
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 19:20:27 +0000