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-rw-r--r--src/io.cpp59
1 files changed, 55 insertions, 4 deletions
diff --git a/src/io.cpp b/src/io.cpp
index bfbfc15..6be01fd 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -135,6 +135,7 @@ std::istream &safeGetline(std::istream &is, std::string &t) {
// Read SNP file. A single column of SNP names.
bool ReadFile_snps(const string file_snps, set<string> &setSnps) {
+ debug_msg("entered");
setSnps.clear();
igzstream infile(file_snps.c_str(), igzstream::in);
@@ -162,6 +163,7 @@ bool ReadFile_snps(const string file_snps, set<string> &setSnps) {
// values for each row are parsed. A valid header can be, for example,
// RS POS CHR
bool ReadFile_snps_header(const string &file_snps, set<string> &setSnps) {
+ debug_msg("entered");
setSnps.clear();
igzstream infile(file_snps.c_str(), igzstream::in);
@@ -187,6 +189,7 @@ bool ReadFile_snps_header(const string &file_snps, set<string> &setSnps) {
continue;
}
ch_ptr = strtok((char *)line.c_str(), " , \t");
+ enforce_msg(ch_ptr,"Problem reading SNP header");
for (size_t i = 0; i < header.coln; i++) {
enforce_msg(ch_ptr,"Problem reading SNP file");
@@ -218,6 +221,7 @@ bool ReadFile_snps_header(const string &file_snps, set<string> &setSnps) {
// Read log file.
bool ReadFile_log(const string &file_log, double &pheno_mean) {
+ debug_msg("ReadFile_log");
ifstream infile(file_log.c_str(), ifstream::in);
if (!infile) {
cout << "error! fail to open log file: " << file_log << endl;
@@ -259,6 +263,7 @@ bool ReadFile_log(const string &file_log, double &pheno_mean) {
bool ReadFile_anno(const string &file_anno, map<string, string> &mapRS2chr,
map<string, long int> &mapRS2bp,
map<string, double> &mapRS2cM) {
+ debug_msg("ReadFile_anno");
mapRS2chr.clear();
mapRS2bp.clear();
@@ -318,6 +323,7 @@ bool ReadFile_anno(const string &file_anno, map<string, string> &mapRS2chr,
// Read 1 column of phenotype.
bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
vector<double> &pheno, const int &p_column) {
+ debug_msg("entered");
indicator_idv.clear();
pheno.clear();
@@ -337,11 +343,11 @@ bool ReadFile_column(const string &file_pheno, vector<int> &indicator_idv,
for (int i = 0; i < (p_column - 1); ++i) {
ch_ptr = strtok(NULL, " , \t");
}
+ enforce_msg(ch_ptr,"Problem reading PHENO column");
if (strcmp(ch_ptr, "NA") == 0) {
indicator_idv.push_back(0);
pheno.push_back(-9);
} else {
-
// Pheno is different from pimass2.
p = atof(ch_ptr);
indicator_idv.push_back(1);
@@ -360,6 +366,7 @@ bool ReadFile_pheno(const string &file_pheno,
vector<vector<int>> &indicator_pheno,
vector<vector<double>> &pheno,
const vector<size_t> &p_column) {
+ debug_msg("entered");
indicator_pheno.clear();
pheno.clear();
@@ -390,7 +397,7 @@ bool ReadFile_pheno(const string &file_pheno,
ch_ptr = strtok((char *)line.c_str(), " , \t");
size_t i = 0;
while (i < p_max) {
- enforce_msg(ch_ptr,"Wrong number of phenotypes");
+ enforce_msg(ch_ptr,"Number of phenotypes out of range");
if (mapP2c.count(i + 1) != 0) {
if (strcmp(ch_ptr, "NA") == 0) {
ind_pheno_row[mapP2c[i + 1]] = 0;
@@ -417,6 +424,7 @@ bool ReadFile_pheno(const string &file_pheno,
bool ReadFile_cvt(const string &file_cvt, vector<int> &indicator_cvt,
vector<vector<double>> &cvt, size_t &n_cvt) {
+ debug_msg("entered");
indicator_cvt.clear();
ifstream infile(file_cvt.c_str(), ifstream::in);
@@ -483,6 +491,7 @@ bool ReadFile_cvt(const string &file_cvt, vector<int> &indicator_cvt,
// Read .bim file.
bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo) {
+ debug_msg("entered");
snpInfo.clear();
ifstream infile(file_bim.c_str(), ifstream::in);
@@ -524,10 +533,11 @@ bool ReadFile_bim(const string &file_bim, vector<SNPINFO> &snpInfo) {
return true;
}
-// Read .fam file.
+// Read .fam file (ignored with -p phenotypes switch)
bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
vector<vector<double>> &pheno, map<string, int> &mapID2num,
const vector<size_t> &p_column) {
+ debug_msg("entered");
indicator_pheno.clear();
pheno.clear();
mapID2num.clear();
@@ -568,6 +578,8 @@ bool ReadFile_fam(const string &file_fam, vector<vector<int>> &indicator_pheno,
size_t i = 0;
while (i < p_max) {
if (mapP2c.count(i + 1) != 0) {
+ enforce_msg(ch_ptr,"Problem reading FAM file (phenotypes out of range)");
+
if (strcmp(ch_ptr, "NA") == 0) {
ind_pheno_row[mapP2c[i + 1]] = 0;
pheno_row[mapP2c[i + 1]] = -9;
@@ -609,6 +621,7 @@ bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
map<string, long int> &mapRS2bp,
map<string, double> &mapRS2cM, vector<SNPINFO> &snpInfo,
size_t &ns_test, bool debug) {
+ debug_msg("entered");
indicator_snp.clear();
snpInfo.clear();
@@ -819,6 +832,7 @@ bool ReadFile_bed(const string &file_bed, const set<string> &setSnps,
const double &maf_level, const double &miss_level,
const double &hwe_level, const double &r2_level,
size_t &ns_test) {
+ debug_msg("entered");
indicator_snp.clear();
size_t ns_total = snpInfo.size();
@@ -1007,6 +1021,7 @@ bool ReadFile_bed(const string &file_bed, const set<string> &setSnps,
// Missing values are replaced by mean.
bool Bimbam_ReadOneSNP(const size_t inc, const vector<int> &indicator_idv,
igzstream &infile, gsl_vector *geno, double &geno_mean) {
+ debug_msg("entered");
size_t ni_total = indicator_idv.size();
string line;
@@ -1057,6 +1072,7 @@ bool Bimbam_ReadOneSNP(const size_t inc, const vector<int> &indicator_idv,
// For PLINK, store SNPs as double too.
void Plink_ReadOneSNP(const int pos, const vector<int> &indicator_idv,
ifstream &infile, gsl_vector *geno, double &geno_mean) {
+ debug_msg("entered");
size_t ni_total = indicator_idv.size(), n_bit;
if (ni_total % 4 == 0) {
n_bit = ni_total / 4;
@@ -1123,6 +1139,7 @@ void Plink_ReadOneSNP(const int pos, const vector<int> &indicator_idv,
void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
map<string, int> &mapID2num, const size_t k_mode, bool &error,
gsl_matrix *G) {
+ debug_msg("entered");
igzstream infile(file_kin.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open kinship file: " << file_kin << endl;
@@ -1239,6 +1256,7 @@ void ReadFile_kin(const string &file_kin, vector<int> &indicator_idv,
void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv,
map<string, int> &mapID2num, const size_t k_mode, bool &error,
gsl_matrix *G) {
+ debug_msg("entered");
igzstream infile(file_mk.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open file: " << file_mk << endl;
@@ -1264,6 +1282,7 @@ void ReadFile_mk(const string &file_mk, vector<int> &indicator_idv,
}
void ReadFile_eigenU(const string &file_ku, bool &error, gsl_matrix *U) {
+ debug_msg("entered");
igzstream infile(file_ku.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open the U file: " << file_ku << endl;
@@ -1312,6 +1331,7 @@ void ReadFile_eigenU(const string &file_ku, bool &error, gsl_matrix *U) {
}
void ReadFile_eigenD(const string &file_kd, bool &error, gsl_vector *eval) {
+ debug_msg("entered");
igzstream infile(file_kd.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open the D file: " << file_kd << endl;
@@ -1360,6 +1380,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps,
vector<int> &indicator_snp, const int k_mode,
const int display_pace, gsl_matrix *matrix_kin,
const bool test_nind) {
+ debug_msg("entered");
igzstream infile(file_geno.c_str(), igzstream::in);
enforce_msg(infile, "error reading genotype file");
@@ -1496,6 +1517,7 @@ bool BimbamKin(const string file_geno, const set<string> ksnps,
bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
const int k_mode, const int display_pace,
gsl_matrix *matrix_kin) {
+ debug_msg("entered");
ifstream infile(file_bed.c_str(), ios::binary);
if (!infile) {
cout << "error reading bed file:" << file_bed << endl;
@@ -1638,6 +1660,7 @@ bool PlinkKin(const string &file_bed, vector<int> &indicator_snp,
bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
const bool calc_K, bool debug) {
+ debug_msg("entered");
igzstream infile(file_geno.c_str(), igzstream::in);
if (!infile) {
cout << "error reading genotype file:" << file_geno << endl;
@@ -1742,6 +1765,7 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
vector<vector<unsigned char>> &Xt, gsl_matrix *K,
const bool calc_K, const size_t ni_test,
const size_t ns_test, bool debug) {
+ debug_msg("entered");
igzstream infile(file_geno.c_str(), igzstream::in);
if (!infile) {
cout << "error reading genotype file:" << file_geno << endl;
@@ -1848,6 +1872,7 @@ bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
vector<int> &indicator_snp, gsl_matrix *UtX, gsl_matrix *K,
const bool calc_K) {
+ debug_msg("entered");
ifstream infile(file_bed.c_str(), ios::binary);
if (!infile) {
cout << "error reading bed file:" << file_bed << endl;
@@ -1979,6 +2004,7 @@ bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
vector<int> &indicator_snp, vector<vector<unsigned char>> &Xt,
gsl_matrix *K, const bool calc_K, const size_t ni_test,
const size_t ns_test) {
+ debug_msg("entered");
ifstream infile(file_bed.c_str(), ios::binary);
if (!infile) {
cout << "error reading bed file:" << file_bed << endl;
@@ -2113,6 +2139,7 @@ bool ReadFile_bed(const string &file_bed, vector<int> &indicator_idv,
bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
map<string, double> &mapRS2est) {
+ debug_msg("entered");
mapRS2est.clear();
ifstream infile(file_est.c_str(), ifstream::in);
@@ -2173,6 +2200,7 @@ bool ReadFile_est(const string &file_est, const vector<size_t> &est_column,
}
bool CountFileLines(const string &file_input, size_t &n_lines) {
+ debug_msg("entered");
igzstream infile(file_input.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open file: " << file_input << endl;
@@ -2189,6 +2217,7 @@ bool CountFileLines(const string &file_input, size_t &n_lines) {
// Read gene expression file.
bool ReadFile_gene(const string &file_gene, vector<double> &vec_read,
vector<SNPINFO> &snpInfo, size_t &ng_total) {
+ debug_msg("entered");
vec_read.clear();
ng_total = 0;
@@ -2252,6 +2281,7 @@ bool ReadFile_sample(const string &file_sample,
vector<vector<double>> &pheno,
const vector<size_t> &p_column, vector<int> &indicator_cvt,
vector<vector<double>> &cvt, size_t &n_cvt) {
+ debug_msg("entered");
indicator_pheno.clear();
pheno.clear();
indicator_cvt.clear();
@@ -2506,6 +2536,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
const double &hwe_level, const double &r2_level,
size_t &ns_test) {
+ debug_msg("entered");
indicator_snp.clear();
ifstream infile(file_bgen.c_str(), ios::binary);
@@ -2793,6 +2824,7 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps,
// Read oxford genotype file and calculate kinship matrix.
bool bgenKin(const string &file_oxford, vector<int> &indicator_snp,
const int k_mode, const int display_pace, gsl_matrix *matrix_kin) {
+ debug_msg("entered");
string file_bgen = file_oxford;
ifstream infile(file_bgen.c_str(), ios::binary);
if (!infile) {
@@ -2851,7 +2883,7 @@ bool bgenKin(const string &file_oxford, vector<int> &indicator_snp,
for (size_t t = 0; t < indicator_snp.size(); ++t) {
if (t % display_pace == 0 || t == (indicator_snp.size() - 1)) {
- ProgressBar("Reading SNPs ", t, indicator_snp.size() - 1);
+ ProgressBar("Reading bgen SNPs ", t, indicator_snp.size() - 1);
}
id.clear();
@@ -2997,6 +3029,7 @@ bool bgenKin(const string &file_oxford, vector<int> &indicator_snp,
// Read header to determine which column contains which item.
bool ReadHeader_io(const string &line, HEADER &header) {
+ debug_msg("entered");
string rs_ptr[] = {"rs", "RS", "snp", "SNP", "snps", "SNPS",
"snpid", "SNPID", "rsid", "RSID", "MarkerName"};
set<string> rs_set(rs_ptr, rs_ptr + 11); // create a set of 11 items
@@ -3264,6 +3297,7 @@ bool ReadHeader_io(const string &line, HEADER &header) {
// it is not included in the analysis.
bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
size_t &n_vc) {
+ debug_msg("entered");
mapRS2cat.clear();
igzstream infile(file_cat.c_str(), igzstream::in);
@@ -3348,6 +3382,7 @@ bool ReadFile_cat(const string &file_cat, map<string, size_t> &mapRS2cat,
bool ReadFile_mcat(const string &file_mcat, map<string, size_t> &mapRS2cat,
size_t &n_vc) {
+ debug_msg("entered");
mapRS2cat.clear();
igzstream infile(file_mcat.c_str(), igzstream::in);
@@ -3386,6 +3421,8 @@ bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
const map<string, size_t> &mapRS2cat,
const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
gsl_matrix *matrix_kin, gsl_vector *vector_ns) {
+ debug_msg("entered");
+ debug_msg("BimbamKinUncentered");
igzstream infile(file_geno.c_str(), igzstream::in);
if (!infile) {
cout << "error reading genotype file:" << file_geno << endl;
@@ -3576,6 +3613,7 @@ bool PlinkKin(const string &file_bed, const int display_pace,
const map<string, size_t> &mapRS2cat,
const vector<SNPINFO> &snpInfo, const gsl_matrix *W,
gsl_matrix *matrix_kin, gsl_vector *vector_ns) {
+ debug_msg("entered");
ifstream infile(file_bed.c_str(), ios::binary);
if (!infile) {
cout << "error reading bed file:" << file_bed << endl;
@@ -3801,6 +3839,7 @@ bool MFILEKin(const size_t mfile_mode, const string &file_mfile,
const map<string, size_t> &mapRS2cat,
const vector<vector<SNPINFO>> &msnpInfo, const gsl_matrix *W,
gsl_matrix *matrix_kin, gsl_vector *vector_ns) {
+ debug_msg("entered");
size_t n_vc = vector_ns->size, ni_test = matrix_kin->size1;
gsl_matrix_set_zero(matrix_kin);
gsl_vector_set_zero(vector_ns);
@@ -3876,6 +3915,7 @@ bool MFILEKin(const size_t mfile_mode, const string &file_mfile,
// Read var file, store mapRS2wsnp.
bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2weight) {
+ debug_msg("entered");
mapRS2weight.clear();
igzstream infile(file_wsnp.c_str(), igzstream::in);
@@ -3901,6 +3941,7 @@ bool ReadFile_wsnp(const string &file_wsnp, map<string, double> &mapRS2weight) {
bool ReadFile_wsnp(const string &file_wcat, const size_t n_vc,
map<string, vector<double>> &mapRS2wvector) {
+ debug_msg("entered");
mapRS2wvector.clear();
igzstream infile(file_wcat.c_str(), igzstream::in);
@@ -3985,6 +4026,7 @@ void ReadFile_beta(const string &file_beta,
vector<size_t> &vec_ni, vector<double> &vec_weight,
vector<double> &vec_z2, size_t &ni_total, size_t &ns_total,
size_t &ns_test) {
+ debug_msg("entered");
vec_cat.clear();
vec_ni.clear();
vec_weight.clear();
@@ -4171,6 +4213,7 @@ void ReadFile_beta(const string &file_beta,
void ReadFile_beta(const string &file_beta, const map<string, double> &mapRS2wA,
map<string, string> &mapRS2A1,
map<string, double> &mapRS2z) {
+ debug_msg("entered");
mapRS2A1.clear();
mapRS2z.clear();
@@ -4332,6 +4375,7 @@ void Calcq(const size_t n_block, const vector<size_t> &vec_cat,
const vector<size_t> &vec_ni, const vector<double> &vec_weight,
const vector<double> &vec_z2, gsl_matrix *Vq, gsl_vector *q,
gsl_vector *s) {
+ debug_msg("entered");
gsl_matrix_set_zero(Vq);
gsl_vector_set_zero(q);
gsl_vector_set_zero(s);
@@ -4485,6 +4529,7 @@ void Calcq(const size_t n_block, const vector<size_t> &vec_cat,
// Read vector file.
void ReadFile_vector(const string &file_vec, gsl_vector *vec) {
+ debug_msg("entered");
igzstream infile(file_vec.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open vector file: " << file_vec << endl;
@@ -4507,6 +4552,7 @@ void ReadFile_vector(const string &file_vec, gsl_vector *vec) {
}
void ReadFile_matrix(const string &file_mat, gsl_matrix *mat) {
+ debug_msg("entered");
igzstream infile(file_mat.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open matrix file: " << file_mat << endl;
@@ -4533,6 +4579,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat) {
void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1,
gsl_matrix *mat2) {
+ debug_msg("entered");
igzstream infile(file_mat.c_str(), igzstream::in);
if (!infile) {
cout << "error! fail to open matrix file: " << file_mat << endl;
@@ -4569,6 +4616,7 @@ void ReadFile_matrix(const string &file_mat, gsl_matrix *mat1,
// Read study file.
void ReadFile_study(const string &file_study, gsl_matrix *Vq_mat,
gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni) {
+ debug_msg("entered");
string Vqfile = file_study + ".Vq.txt";
string sfile = file_study + ".size.txt";
string qfile = file_study + ".q.txt";
@@ -4594,6 +4642,7 @@ void ReadFile_study(const string &file_study, gsl_matrix *Vq_mat,
// Read reference file.
void ReadFile_ref(const string &file_ref, gsl_matrix *S_mat,
gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni) {
+ debug_msg("entered");
string sfile = file_ref + ".size.txt";
string Sfile = file_ref + ".S.txt";
@@ -4617,6 +4666,7 @@ void ReadFile_ref(const string &file_ref, gsl_matrix *S_mat,
// Read mstudy file.
void ReadFile_mstudy(const string &file_mstudy, gsl_matrix *Vq_mat,
gsl_vector *q_vec, gsl_vector *s_vec, size_t &ni) {
+ debug_msg("entered");
gsl_matrix_set_zero(Vq_mat);
gsl_vector_set_zero(q_vec);
gsl_vector_set_zero(s_vec);
@@ -4707,6 +4757,7 @@ void ReadFile_mstudy(const string &file_mstudy, gsl_matrix *Vq_mat,
// Read reference file.
void ReadFile_mref(const string &file_mref, gsl_matrix *S_mat,
gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni) {
+ debug_msg("entered");
gsl_matrix_set_zero(S_mat);
gsl_matrix_set_zero(Svar_mat);
gsl_vector_set_zero(s_vec);
generated by cgit v1.2.3 (git 2.46.2) at 2025-02-01 12:12:29 +0000