diff options
Diffstat (limited to 'gemma.cpp')
| -rw-r--r-- | gemma.cpp | 12 |
1 files changed, 10 insertions, 2 deletions
@@ -61,7 +61,7 @@ using namespace std; GEMMA::GEMMA(void): -version("0.95"), date("08/08/2014"), year("2011") +version("0.95alpha"), date("08/08/2014"), year("2011") {} void GEMMA::PrintHeader (void) @@ -238,6 +238,7 @@ void GEMMA::PrintHelp(size_t option) cout<<" 2: \"id id value\" format"<<endl; cout<<" -n [num] "<<" specify phenotype column in the phenotype/*.fam file (optional; default 1)"<<endl; cout<<" -pace [num] "<<" specify terminal display update pace (default 100000 SNPs or 100000 iterations)."<<endl; + cout<<" -outdir [path] "<<" specify output directory path (default \"./output/\")"<<endl; cout<<" -o [prefix] "<<" specify output file prefix (default \"result\")"<<endl; cout<<" output: prefix.cXX.txt or prefix.sXX.txt from kinship/relatedness matrix estimation"<<endl; cout<<" output: prefix.assoc.txt and prefix.log.txt form association tests"<<endl; @@ -519,6 +520,13 @@ void GEMMA::Assign(int argc, char ** argv, PARAM &cPar) str.assign(argv[i]); cPar.d_pace=atoi(str.c_str()); } + else if (strcmp(argv[i], "-outdir")==0) { + if(argv[i+1] == NULL || argv[i+1][0] == '-') {continue;} + ++i; + str.clear(); + str.assign(argv[i]); + cPar.path_out=str; + } else if (strcmp(argv[i], "-o")==0) { if(argv[i+1] == NULL || argv[i+1][0] == '-') {continue;} ++i; @@ -1567,7 +1575,7 @@ void GEMMA::BatchRun (PARAM &cPar) void GEMMA::WriteLog (int argc, char ** argv, PARAM &cPar) { string file_str; - file_str="./output/"+cPar.file_out; + file_str=cPar.path_out+"/"+cPar.file_out; file_str+=".log.txt"; ofstream outfile (file_str.c_str(), ofstream::out); |