diff options
Diffstat (limited to 'src/param.cpp')
| -rw-r--r-- | src/param.cpp | 59 |
1 files changed, 43 insertions, 16 deletions
diff --git a/src/param.cpp b/src/param.cpp index 0a1d721..a7be178 100644 --- a/src/param.cpp +++ b/src/param.cpp @@ -208,7 +208,6 @@ void PARAM::ReadFiles (void) { ns_total=indicator_snp.size(); } - // Read genotype and phenotype file for PLINK format. if (!file_bfile.empty()) { file_str=file_bfile+".bim"; @@ -348,8 +347,6 @@ void PARAM::ReadFiles (void) { infile.clear(); } - - // Read genotype and phenotype file for multiple BIMBAM files. if (!file_mgeno.empty()) { @@ -403,8 +400,6 @@ void PARAM::ReadFiles (void) { infile.clear(); } - - if (!file_gene.empty()) { if (ReadFile_pheno (file_pheno, indicator_pheno, pheno, p_column)==false) {error=true;} @@ -433,7 +428,6 @@ void PARAM::ReadFiles (void) { } } - // Read is after gene file. if (!file_read.empty() ) { if (ReadFile_column (file_read, indicator_read, @@ -471,8 +465,7 @@ void PARAM::ReadFiles (void) { return; } -void PARAM::CheckParam (void) -{ +void PARAM::CheckParam (void) { struct stat fileInfo; string str; @@ -482,15 +475,49 @@ void PARAM::CheckParam (void) k_mode<<endl; error=true; } - if (a_mode!=1 && a_mode!=2 && a_mode!=3 && a_mode!=4 && a_mode!=5 && a_mode!=11 && a_mode!=12 && a_mode!=13 && a_mode!=14 && a_mode!=15 && a_mode!=21 && a_mode!=22 && a_mode!=25 && a_mode!=26 && a_mode!=27 && a_mode!=28 && a_mode!=31 && a_mode!=41 && a_mode!=42 && a_mode!=43 && a_mode!=51 && a_mode!=52 && a_mode!=53 && a_mode!=54 && a_mode!=61 && a_mode!=62 && a_mode!=63 && a_mode!=66 && a_mode!=67 && a_mode!=71) - {cout<<"error! unknown analysis mode: "<<a_mode<<". make sure -gk or -eigen or -lmm or -bslmm -predict or -calccov is sepcified correctly."<<endl; error=true;} - if (miss_level>1) {cout<<"error! missing level needs to be between 0 and 1. current value = "<<miss_level<<endl; error=true;} - if (maf_level>0.5) {cout<<"error! maf level needs to be between 0 and 0.5. current value = "<<maf_level<<endl; error=true;} - if (hwe_level>1) {cout<<"error! hwe level needs to be between 0 and 1. current value = "<<hwe_level<<endl; error=true;} - if (r2_level>1) {cout<<"error! r2 level needs to be between 0 and 1. current value = "<<r2_level<<endl; error=true;} + if (a_mode!=1 && a_mode!=2 && a_mode!=3 && a_mode!=4 && a_mode!=5 + && a_mode!=11 && a_mode!=12 && a_mode!=13 && a_mode!=14 && + a_mode!=15 && a_mode!=21 && a_mode!=22 && a_mode!=25 && + a_mode!=26 && a_mode!=27 && a_mode!=28 && a_mode!=31 && + a_mode!=41 && a_mode!=42 && a_mode!=43 && a_mode!=51 && + a_mode!=52 && a_mode!=53 && a_mode!=54 && a_mode!=61 && + a_mode!=62 && a_mode!=63 && a_mode!=66 && a_mode!=67 && + a_mode!=71) { + cout<<"error! unknown analysis mode: "<<a_mode<< + ". make sure -gk or -eigen or -lmm or -bslmm -predict or " << + "-calccov is sepcified correctly."<<endl; + error=true; + } + if (miss_level>1) { + cout<<"error! missing level needs to be between 0 and 1. " << + "current value = "<<miss_level<<endl; + error=true; + } + if (maf_level>0.5) { + cout<<"error! maf level needs to be between 0 and 0.5. " << + "current value = "<<maf_level<<endl; + error=true; + } + if (hwe_level>1) { + cout<<"error! hwe level needs to be between 0 and 1. " << + "current value = "<<hwe_level<<endl; + error=true; + } + if (r2_level>1) { + cout<<"error! r2 level needs to be between 0 and 1. " << + "current value = "<<r2_level<<endl; + error=true; + } - if (l_max<l_min) {cout<<"error! maximum lambda value must be larger than the minimal value. current values = "<<l_max<<" and "<<l_min<<endl; error=true;} - if (h_max<h_min) {cout<<"error! maximum h value must be larger than the minimal value. current values = "<<h_max<<" and "<<h_min<<endl; error=true;} + if (l_max<l_min) { + cout<<"error! maximum lambda value must be larger than the " << + "minimal value. current values = "<<l_max<<" and "<<l_min<<endl; + error=true; + } + if (h_max<h_min) { + cout<<"error! maximum h value must be larger than the minimal value. current values = "<<h_max<<" and "<<h_min<<endl; + error=true; + } if (s_max<s_min) {cout<<"error! maximum s value must be larger than the minimal value. current values = "<<s_max<<" and "<<s_min<<endl; error=true;} if (rho_max<rho_min) {cout<<"error! maximum rho value must be larger than the minimal value. current values = "<<rho_max<<" and "<<rho_min<<endl; error=true;} if (logp_max<logp_min) {cout<<"error! maximum logp value must be larger than the minimal value. current values = "<<logp_max/log(10)<<" and "<<logp_min/log(10)<<endl; error=true;} |