diff options
Diffstat (limited to 'src/gemma.cpp')
| -rw-r--r-- | src/gemma.cpp | 29 |
1 files changed, 9 insertions, 20 deletions
diff --git a/src/gemma.cpp b/src/gemma.cpp index 7d12055..cb01ee0 100644 --- a/src/gemma.cpp +++ b/src/gemma.cpp @@ -48,6 +48,7 @@ extern "C" { #include "bslmm.h" #include "bslmmdap.h" +#include <csignal> // for gsl_error_handler #include "gemma.h" #include "gemma_io.h" #include "lapack.h" @@ -64,23 +65,6 @@ extern "C" { using namespace std; -// OPTIONS -// ------- -// gk: 21-22 -// gs: 25-26 -// gq: 27-28 -// eigen: 31-32 -// lmm: 1-5 -// bslmm: 11-15 -// predict: 41-43 -// lm: 51 -// vc: 61 -// ci: 66-67 -// calccor: 71 -// gw: 72 - -enum M_MODE { M_LMM1=1, M_LMM2=2, M_LMM3=3, M_LMM4=4, M_LMM5=5, M_KIN=21, M_KIN2=22, M_EIGEN=31 }; - GEMMA::GEMMA(void) : version(GEMMA_VERSION), date(GEMMA_DATE), year(GEMMA_YEAR) {} void gemma_gsl_error_handler (const char * reason, @@ -88,7 +72,7 @@ void gemma_gsl_error_handler (const char * reason, int line, int gsl_errno) { cerr << "GSL ERROR: " << reason << " in " << file << " at line " << line << " errno " << gsl_errno <<endl; - exit(22); + std::raise(SIGINT); // keep the stack trace for gdb } #if defined(OPENBLAS) && !defined(OPENBLAS_LEGACY) @@ -737,6 +721,7 @@ void GEMMA::PrintHelp(size_t option) { cout << " -strict strict mode will stop when there is a problem" << endl; cout << " -silence silent terminal display" << endl; cout << " -debug debug output" << endl; + cout << " -debug-data debug data output" << endl; cout << " -nind [num] read up to num individuals" << endl; cout << " -issue [num] enable tests relevant to issue tracker" << endl; cout << " -legacy run gemma in legacy mode" << endl; @@ -1611,6 +1596,10 @@ void GEMMA::Assign(int argc, char **argv, PARAM &cPar) { str.clear(); str.assign(argv[i]); cPar.window_ns = atoi(str.c_str()); + } else if (strcmp(argv[i], "-debug-data") == 0) { + // cPar.mode_debug = true; + debug_set_debug_data_mode(true); + debug_set_debug_mode(true); } else if (strcmp(argv[i], "-debug") == 0) { // cPar.mode_debug = true; debug_set_debug_mode(true); @@ -1780,7 +1769,7 @@ void GEMMA::BatchRun(PARAM &cPar) { cout << "Start Eigen-Decomposition..." << endl; time_start = clock(); cPar.trace_G = EigenDecomp_Zeroed(G, U, eval, 0); - write(eval,"eval zeroed"); + // write(eval,"eval zeroed"); cPar.time_eigen = (clock() - time_start) / (double(CLOCKS_PER_SEC) * 60.0); // calculate UtW and Uty @@ -2625,7 +2614,7 @@ void GEMMA::BatchRun(PARAM &cPar) { } else { cPar.trace_G = EigenDecomp_Zeroed(G, U, eval, 0); } - write(eval,"eval"); + // write(eval,"eval"); if (!cPar.file_weight.empty()) { double wi; |