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-rw-r--r--src/vc.cpp43
1 files changed, 23 insertions, 20 deletions
diff --git a/src/vc.cpp b/src/vc.cpp
index 1465f16..1a16c07 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -41,7 +41,7 @@
#include "gsl/gsl_min.h"
#include "gsl/gsl_multiroots.h"
-#include "Eigen/Dense"
+// #include "Eigen/Dense"
#include "eigenlib.h"
#include "gzstream.h"
@@ -53,7 +53,7 @@
#include "vc.h"
using namespace std;
-using namespace Eigen;
+// using namespace Eigen;
// In this file, X, Y are already transformed (i.e. UtX and UtY).
void VC::CopyFromParam(PARAM &cPar) {
@@ -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;
}
@@ -1932,7 +1935,7 @@ void VC::CalcVCacl(const gsl_matrix *K, const gsl_matrix *W,
size_t n1 = K->size1, n2 = K->size2;
size_t n_vc = n2 / n1;
- double d, y2_sum, tau_inv, se_tau_inv;
+ double d, y2_sum, tau_inv;
// New matrices/vectors.
gsl_matrix *K_scale = gsl_matrix_alloc(n1, n2);
@@ -2131,7 +2134,7 @@ void VC::CalcVCacl(const gsl_matrix *K, const gsl_matrix *W,
// Compute variance for tau_inv.
gsl_blas_dgemv(CblasNoTrans, 1.0, V_mat, y_scale, 0.0, n1_vec);
gsl_blas_ddot(y_scale, n1_vec, &d);
- se_tau_inv = sqrt(2 * d) / (double)n1;
+ // auto se_tau_inv = sqrt(2 * d) / (double)n1; UNUSED
// Transform pve back to the original scale and save data.
v_pve.clear();
@@ -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++;
generated by cgit v1.2.3 (git 2.44.0) at 2025-01-19 17:56:28 +0000