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-rw-r--r--src/debug.cpp11
-rw-r--r--src/debug.h3
-rw-r--r--src/io.cpp106
-rw-r--r--src/lmm.cpp29
4 files changed, 84 insertions, 65 deletions
diff --git a/src/debug.cpp b/src/debug.cpp
index 45e57d7..4e58d5d 100644
--- a/src/debug.cpp
+++ b/src/debug.cpp
@@ -141,10 +141,15 @@ gsl_vector *gsl_vector_safe_alloc(size_t n) {
return v;
}
-char *do_strtok_safe(char *tokenize, const char *delimiters, const char *__pretty_function, const char *__file, int __line) {
+char *do_strtok_safe(char *tokenize, const char *delimiters, const char *__pretty_function, const char *__file, int __line,
+ const char *infile) {
auto token = strtok(tokenize,delimiters);
- if (token == NULL && is_check_mode())
- fail_at_msg(__file,__line,string("strtok failed in ") + __pretty_function);
+ if (token == NULL) {
+ if (infile)
+ fail_at_msg(__file,__line,string("Parsing input file '") + infile + "' failed in function " + __pretty_function);
+ else
+ fail_at_msg(__file,__line,string("Parsing input file failed in function ") + __pretty_function);
+ }
return token;
}
diff --git a/src/debug.h b/src/debug.h
index 208868e..67764df 100644
--- a/src/debug.h
+++ b/src/debug.h
@@ -59,7 +59,8 @@ int gsl_vector_safe_memcpy (gsl_vector *dest, const gsl_vector *src);
void gsl_vector_safe_free (gsl_vector *v);
void do_gsl_vector_safe_free (gsl_vector *v, const char *__pretty_function, const char *__file, int __line);
-char *do_strtok_safe(char *tokenize, const char *delimiters, const char *__pretty_function, const char *__file, int __line);
+char *do_strtok_safe(char *tokenize, const char *delimiters, const char *__pretty_function, const char *__file, int __line, const char *infile = NULL);
+#define strtok_safe2(string,delimiters,infile) do_strtok_safe(string,delimiters,__SHOW_FUNC,__FILE__,__LINE__,infile)
#define strtok_safe(string,delimiters) do_strtok_safe(string,delimiters,__SHOW_FUNC,__FILE__,__LINE__)
// Validation routines
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));
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 4198fab..5822275 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -1209,12 +1209,12 @@ void LMM::AnalyzeGene(const gsl_matrix *U, const gsl_vector *eval,
if (t % d_pace == 0 || t == ng_total - 1) {
ProgressBar("Performing Analysis", t, ng_total - 1);
}
- 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;
c_phen = 0;
for (size_t i = 0; i < indicator_idv.size(); ++i) {
- ch_ptr = strtok_safe(NULL, " , \t");
+ ch_ptr = strtok_safe2(NULL, " , \t",file_gene.c_str());
if (indicator_idv[i] == 0) {
continue;
}
@@ -1465,8 +1465,9 @@ void LMM::AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval,
const gsl_matrix *W, const gsl_vector *y,
const set<string> gwasnps) {
debug_msg(file_geno);
+ auto infilen = file_geno.c_str();
- igzstream infile(file_geno.c_str(), igzstream::in);
+ igzstream infile(infilen, igzstream::in);
enforce_msg(infile, "error reading genotype file");
size_t prev_line = 0;
@@ -1481,18 +1482,17 @@ void LMM::AnalyzeBimbam(const gsl_matrix *U, const gsl_vector *eval,
safeGetline(infile, line);
prev_line++;
}
- char *ch_ptr = strtok((char *)line.c_str(), " , \t");
- enforce_msg(ch_ptr, "Parsing BIMBAM genofile"); // ch_ptr should not be NULL
+ char *ch_ptr = strtok_safe2((char *)line.c_str(), " , \t",infilen);
+ // enforce_msg(ch_ptr, "Parsing BIMBAM genofile"); // ch_ptr should not be NULL
auto snp = string(ch_ptr);
- ch_ptr = strtok_safe(NULL, " , \t"); // skip column
- ch_ptr = strtok_safe(NULL, " , \t"); // skip column
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen); // skip column
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen); // skip column
gs.assign (ni_total,nan("")); // wipe values
for (size_t i = 0; i < ni_total; ++i) {
- ch_ptr = strtok(NULL, " , \t");
- enforce_msg(ch_ptr,line.c_str());
+ ch_ptr = strtok_safe2(NULL, " , \t",infilen);
if (strcmp(ch_ptr, "NA") != 0)
gs[i] = atof(ch_ptr);
}
@@ -1913,7 +1913,8 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval,
const gsl_matrix *W, const gsl_vector *y,
const gsl_vector *env) {
debug_msg("entering");
- igzstream infile(file_geno.c_str(), igzstream::in);
+ auto infilen = file_gene.c_str();
+ igzstream infile(infilen, igzstream::in);
if (!infile) {
cout << "error reading genotype file:" << file_geno << endl;
return;
@@ -1957,16 +1958,16 @@ void LMM::AnalyzeBimbamGXE(const gsl_matrix *U, const gsl_vector *eval,
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);
x_mean = 0.0;
c_phen = 0;
n_miss = 0;
gsl_vector_set_zero(x_miss);
for (size_t 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;
}
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-18 22:53:44 +0000