diff options
| -rw-r--r-- | src/gemma.cpp | 4 | ||||
| -rw-r--r-- | src/io.cpp | 9 |
2 files changed, 8 insertions, 5 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index e3fb005..2af8f8e 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -299,7 +299,7 @@ void GEMMA::PrintHelp(size_t option) { cout << " ..." << endl; cout << " missing value: NA" << endl; cout << " -p [filename] " - << " specify input BIMBAM phenotype file name" << endl; + << " specify input BIMBAM-style phenotype file name (when used with PLINK .fam phenotypes are ignored)" << endl; cout << " format: phenotype for individual 1" << endl; cout << " phenotype for individual 2" << endl; cout << " ..." << endl; @@ -1044,7 +1044,7 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) { str.clear(); str.assign(argv[i]); cPar.k_mode = atoi(str.c_str()); - } else if (strcmp(argv[i], "-n") == 0) { // set pheno column (range) + } else if (strcmp(argv[i], "-n") == 0) { // set pheno column (list/range) (cPar.p_column).clear(); while (argv[i + 1] != NULL && argv[i + 1][0] != '-') { ++i; @@ -187,6 +187,7 @@ 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"); @@ -337,11 +338,11 @@ 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); @@ -390,7 +391,7 @@ 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; @@ -524,7 +525,7 @@ 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) { @@ -568,6 +569,8 @@ 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; |