| /dports/biology/gemma/GEMMA-0.98.3/src/ |
| H A D | ldr.cpp | 54 file_geno = cPar.file_geno; in CopyFromParam()
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| H A D | gemma_io.h | 62 bool ReadFile_geno(const string &file_geno, const set<string> &setSnps,
90 bool BimbamKin(const string file_geno, const set<string> ksnps,
97 bool ReadFile_geno(const string file_geno, vector<int> &indicator_idv,
103 bool ReadFile_geno(const string &file_geno, vector<int> &indicator_idv,
132 bool BimbamKinUncentered(const string &file_geno, const set<string> ksnps,
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| H A D | varcov.cpp | 52 file_geno = cPar.file_geno; in CopyFromParam()
251 igzstream infile(file_geno.c_str(), igzstream::in); in AnalyzeBimbam()
253 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbam()
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| H A D | param.cpp | 182 if (!file_geno.empty()) { in ReadFiles()
188 if (CountFileLines(file_geno, ns_total) == false) { in ReadFiles()
292 if (!file_geno.empty()) { in ReadFiles()
486 if (file_geno.empty() && file_gene.empty() && !file_pheno.empty()) { in ReadFiles()
714 if ((!file_geno.empty() || !file_gene.empty())) { in CheckParam()
722 str = file_geno; in CheckParam()
817 if (!file_geno.empty()) { in CheckParam()
943 if (k_mode == 2 && !file_geno.empty()) { in CheckParam()
1311 file_str = file_geno; in CalcKin()
1740 } else if (!file_geno.empty()) { in CalcS()
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| H A D | vc.h | 99 bool BimbamXwz(const string &file_geno, const int display_pace,
113 bool BimbamXtXwz(const string &file_geno, const int display_pace,
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| H A D | prdt.cpp | 47 file_geno = cPar.file_geno; in CopyFromParam()
209 igzstream infile(file_geno.c_str(), igzstream::in); in AnalyzeBimbam()
211 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbam()
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| H A D | ldr.h | 38 string file_geno; variable
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| H A D | varcov.h | 35 string file_geno; variable
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| H A D | prdt.h | 39 string file_geno; variable
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| H A D | lm.h | 37 string file_geno; variable
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| H A D | lm.cpp | 54 file_geno = cPar.file_geno; in CopyFromParam()
384 igzstream infile(file_geno.c_str(), igzstream::in); in AnalyzeBimbam()
386 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbam()
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| H A D | gemma_io.cpp | 647 igzstream infile(file_geno.c_str(), igzstream::in); in ReadFile_geno()
649 cout << "error reading genotype file:" << file_geno << endl; in ReadFile_geno()
695 auto infilen = file_geno.c_str(); in ReadFile_geno()
742 auto infilen = file_geno.c_str(); in ReadFile_geno()
1406 auto infilen = file_geno.c_str(); in BimbamKin()
1729 igzstream infile(file_geno.c_str(), igzstream::in); in ReadFile_geno()
1754 auto infilen = file_geno.c_str(); in ReadFile_geno()
1835 igzstream infile(file_geno.c_str(), igzstream::in); in ReadFile_geno()
1864 auto infilen = file_geno.c_str(); in ReadFile_geno()
2746 igzstream infile(file_geno.c_str(), igzstream::in); in BimbamKinUncentered()
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| H A D | mvlmm.h | 37 string file_geno; variable
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| H A D | bslmmdap.h | 38 string file_geno; variable
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| H A D | lmm.h | 57 string file_geno; variable
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| H A D | bslmm.h | 39 string file_geno; variable
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| H A D | param.h | 134 string file_geno, file_mgeno; variable
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| H A D | gemma.cpp | 785 cPar.file_geno = str; in Assign()
2482 } else if (!cPar.file_geno.empty()) { in BatchRun()
2483 BimbamXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun()
2503 } else if (!cPar.file_geno.empty()) { in BatchRun()
2504 BimbamXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun()
2522 } else if (!cPar.file_geno.empty()) { in BatchRun()
2523 BimbamXtXwz(cPar.file_geno, cPar.d_pace, cPar.indicator_idv, in BatchRun()
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| H A D | vc.cpp | 2220 bool BimbamXwz(const string &file_geno, const int display_pace, in BimbamXwz() argument
2225 igzstream infile(file_geno.c_str(), igzstream::in); in BimbamXwz()
2227 cout << "error reading genotype file:" << file_geno << endl; in BimbamXwz()
2477 bool BimbamXtXwz(const string &file_geno, const int display_pace, in BimbamXtXwz() argument
2481 igzstream infile(file_geno.c_str(), igzstream::in); in BimbamXtXwz()
2483 cout << "error reading genotype file:" << file_geno << endl; in BimbamXtXwz()
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| H A D | lmm.cpp | 58 file_geno = cPar.file_geno; in CopyFromParam()
1652 debug_msg(file_geno); in AnalyzeBimbam()
1653 auto infilen = file_geno.c_str(); in AnalyzeBimbam()
2235 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbamGXE()
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| H A D | bslmm.cpp | 55 file_geno = cPar.file_geno; in CopyFromParam()
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| H A D | mvlmm.cpp | 56 file_geno = cPar.file_geno; in CopyFromParam()
2974 igzstream infile(file_geno.c_str(), igzstream::in); in AnalyzeBimbam()
2976 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbam()
3959 igzstream infile(file_geno.c_str(), igzstream::in); in AnalyzeBimbamGXE()
3961 cout << "error reading genotype file:" << file_geno << endl; in AnalyzeBimbamGXE()
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