diff options
Diffstat (limited to 'src/vc.cpp')
| -rw-r--r-- | src/vc.cpp | 35 |
1 files changed, 19 insertions, 16 deletions
diff --git a/src/vc.cpp b/src/vc.cpp index f8cc2b5..f4cd650 100644 --- a/src/vc.cpp +++ b/src/vc.cpp @@ -663,7 +663,7 @@ void ReadFile_cor(const string &file_cor, const set<string> &setSnps, HEADER header; // Header. - !safeGetline(infile, line).eof(); + safeGetline(infile, line).eof(); ReadHeader_vc(line, header); if (header.n_col == 0) { @@ -678,7 +678,7 @@ void ReadFile_cor(const string &file_cor, const set<string> &setSnps, while (!safeGetline(infile, line).eof()) { // do not read cor values this time; upto col_n-1. - ch_ptr = strtok((char *)line.c_str(), " , \t"); + ch_ptr = strtok_safe((char *)line.c_str(), " , \t"); n_total = 0; n_mis = 0; @@ -688,6 +688,7 @@ void ReadFile_cor(const string &file_cor, const set<string> &setSnps, d_cm = 0; d_pos = 0; for (size_t i = 0; i < header.coln - 1; i++) { + enforce(ch_ptr); if (header.rs_col != 0 && header.rs_col == i + 1) { rs = ch_ptr; } @@ -822,7 +823,7 @@ void ReadFile_beta(const bool flag_priorscale, const string &file_beta, // Read header. HEADER header; - !safeGetline(infile, line).eof(); + safeGetline(infile, line).eof(); ReadHeader_vc(line, header); if (header.n_col == 0) { @@ -844,7 +845,7 @@ void ReadFile_beta(const bool flag_priorscale, const string &file_beta, } while (!safeGetline(infile, line).eof()) { - ch_ptr = strtok((char *)line.c_str(), " , \t"); + ch_ptr = strtok_safe((char *)line.c_str(), " , \t"); z = 0; beta = 0; @@ -857,6 +858,7 @@ void ReadFile_beta(const bool flag_priorscale, 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; } @@ -1055,7 +1057,7 @@ void ReadFile_cor(const string &file_cor, const vector<string> &vec_rs, // Header. HEADER header; - !safeGetline(infile, line).eof(); + safeGetline(infile, line).eof(); ReadHeader_vc(line, header); while (!safeGetline(infile, line).eof()) { @@ -1063,8 +1065,9 @@ void ReadFile_cor(const string &file_cor, const vector<string> &vec_rs, // Do not read cor values this time; upto col_n-1. d_pos1 = 0; d_cm1 = 0; - ch_ptr = strtok((char *)line.c_str(), " , \t"); + ch_ptr = strtok_safe((char *)line.c_str(), " , \t"); for (size_t i = 0; i < header.coln - 1; i++) { + enforce(ch_ptr); if (header.rs_col != 0 && header.rs_col == i + 1) { rs = ch_ptr; } @@ -2238,7 +2241,7 @@ bool BimbamXwz(const string &file_geno, const int display_pace, gsl_vector_mul(wz, w); 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); } @@ -2246,9 +2249,9 @@ bool BimbamXwz(const string &file_geno, const int display_pace, 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"); geno_mean = 0.0; n_miss = 0; @@ -2260,7 +2263,7 @@ bool BimbamXwz(const string &file_geno, const int display_pace, 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++; @@ -2491,7 +2494,7 @@ bool BimbamXtXwz(const string &file_geno, const int display_pace, gsl_vector *geno_miss = gsl_vector_alloc(ni_test); 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); } @@ -2499,9 +2502,9 @@ bool BimbamXtXwz(const string &file_geno, const int display_pace, 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"); geno_mean = 0.0; n_miss = 0; @@ -2513,7 +2516,7 @@ bool BimbamXtXwz(const string &file_geno, const int display_pace, 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++; |