Jason W. Bacon
189 lines
9.7 KiB
C++
189 lines
9.7 KiB
C++
--- src/gemma.cpp.orig 2018-12-11 05:34:29 UTC
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+++ src/gemma.cpp
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@@ -75,9 +75,9 @@ void gemma_gsl_error_handler (const char * reason,
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std::raise(SIGINT); // keep the stack trace for gdb
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}
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-#if defined(OPENBLAS) && !defined(OPENBLAS_LEGACY)
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-#include <openblas_config.h>
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-#endif
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+//#if defined(OPENBLAS) && !defined(OPENBLAS_LEGACY)
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+//#include <openblas_config.h>
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+//#endif
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void GEMMA::PrintHeader(void) {
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@@ -154,7 +154,7 @@ void GEMMA::PrintHelp(size_t option) {
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if (option == 0) {
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cout << endl;
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- cout << " type ./gemma -h [num] for detailed help" << endl;
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+ cout << " type gemma -h [num] for detailed help" << endl;
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cout << " options: " << endl;
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cout << " 1: quick guide" << endl;
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cout << " 2: file I/O related" << endl;
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@@ -176,116 +176,116 @@ void GEMMA::PrintHelp(size_t option) {
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if (option == 1) {
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cout << " QUICK GUIDE" << endl;
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cout << " to generate a relatedness matrix: " << endl;
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- cout << " ./gemma -bfile [prefix] -gk [num] -o [prefix]" << endl;
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- cout << " ./gemma -g [filename] -p [filename] -gk [num] -o [prefix]"
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+ cout << " gemma -bfile [prefix] -gk [num] -o [prefix]" << endl;
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+ cout << " gemma -g [filename] -p [filename] -gk [num] -o [prefix]"
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<< endl;
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cout << " to generate the S matrix: " << endl;
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- cout << " ./gemma -bfile [prefix] -gs -o [prefix]" << endl;
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- cout << " ./gemma -p [filename] -g [filename] -gs -o [prefix]"
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+ cout << " gemma -bfile [prefix] -gs -o [prefix]" << endl;
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+ cout << " gemma -p [filename] -g [filename] -gs -o [prefix]"
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<< endl;
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- cout << " ./gemma -bfile [prefix] -cat [filename] -gs -o [prefix]"
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+ cout << " gemma -bfile [prefix] -cat [filename] -gs -o [prefix]"
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<< endl;
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- cout << " ./gemma -p [filename] -g [filename] -cat [filename] -gs "
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+ cout << " gemma -p [filename] -g [filename] -cat [filename] -gs "
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"-o [prefix]"
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<< endl;
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- cout << " ./gemma -bfile [prefix] -sample [num] -gs -o [prefix]"
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+ cout << " gemma -bfile [prefix] -sample [num] -gs -o [prefix]"
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<< endl;
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- cout << " ./gemma -p [filename] -g [filename] -sample [num] -gs -o "
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+ cout << " gemma -p [filename] -g [filename] -sample [num] -gs -o "
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"[prefix]"
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<< endl;
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cout << " to generate the q vector: " << endl;
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- cout << " ./gemma -beta [filename] -gq -o [prefix]" << endl;
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- cout << " ./gemma -beta [filename] -cat [filename] -gq -o [prefix]"
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+ cout << " gemma -beta [filename] -gq -o [prefix]" << endl;
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+ cout << " gemma -beta [filename] -cat [filename] -gq -o [prefix]"
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<< endl;
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cout << " to generate the ldsc weigthts: " << endl;
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- cout << " ./gemma -beta [filename] -gw -o [prefix]" << endl;
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- cout << " ./gemma -beta [filename] -cat [filename] -gw -o [prefix]"
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+ cout << " gemma -beta [filename] -gw -o [prefix]" << endl;
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+ cout << " gemma -beta [filename] -cat [filename] -gw -o [prefix]"
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<< endl;
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cout << " to perform eigen decomposition of the relatedness matrix: "
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<< endl;
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- cout << " ./gemma -bfile [prefix] -k [filename] -eigen -o [prefix]"
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+ cout << " gemma -bfile [prefix] -k [filename] -eigen -o [prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -k [filename] -eigen "
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+ cout << " gemma -g [filename] -p [filename] -k [filename] -eigen "
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"-o [prefix]"
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<< endl;
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cout << " to estimate variance components: " << endl;
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- cout << " ./gemma -bfile [prefix] -k [filename] -vc [num] -o "
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+ cout << " gemma -bfile [prefix] -k [filename] -vc [num] -o "
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"[prefix]"
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<< endl;
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- cout << " ./gemma -p [filename] -k [filename] -vc [num] -o [prefix]"
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+ cout << " gemma -p [filename] -k [filename] -vc [num] -o [prefix]"
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<< endl;
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- cout << " ./gemma -bfile [prefix] -mk [filename] -vc [num] -o "
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+ cout << " gemma -bfile [prefix] -mk [filename] -vc [num] -o "
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"[prefix]"
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<< endl;
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cout
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- << " ./gemma -p [filename] -mk [filename] -vc [num] -o [prefix]"
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- << endl;
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- cout << " ./gemma -beta [filename] -cor [filename] -vc [num] -o "
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+ << " gemma -p [filename] -mk [filename] -vc [num] -o [prefix]"
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+ << endl;
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+ cout << " gemma -beta [filename] -cor [filename] -vc [num] -o "
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"[prefix]"
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<< endl;
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- cout << " ./gemma -beta [filename] -cor [filename] -cat [filename] "
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+ cout << " gemma -beta [filename] -cor [filename] -cat [filename] "
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"-vc [num] -o [prefix]"
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<< endl;
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cout << " options for the above two commands: -crt -windowbp [num]"
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<< endl;
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- cout << " ./gemma -mq [filename] -ms [filename] -mv [filename] -vc "
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+ cout << " gemma -mq [filename] -ms [filename] -mv [filename] -vc "
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"[num] -o [prefix]"
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<< endl;
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cout << " or with summary statistics, replace bfile with mbfile, "
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"or g or mg; vc=1 for HE weights and vc=2 for LDSC weights"
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<< endl;
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- cout << " ./gemma -beta [filename] -bfile [filename] -cat "
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+ cout << " gemma -beta [filename] -bfile [filename] -cat "
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"[filename] -wsnp [filename] -wcat [filename] -vc [num] -o [prefix]"
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<< endl;
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- cout << " ./gemma -beta [filename] -bfile [filename] -cat "
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+ cout << " gemma -beta [filename] -bfile [filename] -cat "
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"[filename] -wsnp [filename] -wcat [filename] -ci [num] -o [prefix]"
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<< endl;
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cout << " to fit a linear mixed model: " << endl;
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- cout << " ./gemma -bfile [prefix] -k [filename] -lmm [num] -o "
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+ cout << " gemma -bfile [prefix] -k [filename] -lmm [num] -o "
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"[prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -a [filename] -k "
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+ cout << " gemma -g [filename] -p [filename] -a [filename] -k "
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"[filename] -lmm [num] -o [prefix]"
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<< endl;
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cout << " to fit a linear mixed model to test g by e effects: " << endl;
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- cout << " ./gemma -bfile [prefix] -gxe [filename] -k [filename] "
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+ cout << " gemma -bfile [prefix] -gxe [filename] -k [filename] "
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"-lmm [num] -o [prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -a [filename] -gxe "
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+ cout << " gemma -g [filename] -p [filename] -a [filename] -gxe "
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"[filename] -k [filename] -lmm [num] -o [prefix]"
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<< endl;
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cout << " to fit a univariate linear mixed model with different residual "
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"weights for different individuals: "
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<< endl;
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- cout << " ./gemma -bfile [prefix] -weight [filename] -k [filename] "
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+ cout << " gemma -bfile [prefix] -weight [filename] -k [filename] "
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"-lmm [num] -o [prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -a [filename] "
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+ cout << " gemma -g [filename] -p [filename] -a [filename] "
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"-weight [filename] -k [filename] -lmm [num] -o [prefix]"
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<< endl;
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cout << " to fit a multivariate linear mixed model: " << endl;
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- cout << " ./gemma -bfile [prefix] -k [filename] -lmm [num] -n "
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+ cout << " gemma -bfile [prefix] -k [filename] -lmm [num] -n "
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"[pheno cols...] -o [prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -a [filename] -k "
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+ cout << " gemma -g [filename] -p [filename] -a [filename] -k "
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"[filename] -lmm [num] -n [pheno cols...] -o [prefix]"
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<< endl;
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cout << " to fit a Bayesian sparse linear mixed model: " << endl;
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- cout << " ./gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl;
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- cout << " ./gemma -g [filename] -p [filename] -a [filename] -bslmm "
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+ cout << " gemma -bfile [prefix] -bslmm [num] -o [prefix]" << endl;
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+ cout << " gemma -g [filename] -p [filename] -a [filename] -bslmm "
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"[num] -o [prefix]"
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<< endl;
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cout << " to obtain predicted values: " << endl;
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- cout << " ./gemma -bfile [prefix] -epm [filename] -emu [filename] "
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+ cout << " gemma -bfile [prefix] -epm [filename] -emu [filename] "
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"-ebv [filename] -k [filename] -predict [num] -o [prefix]"
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<< endl;
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- cout << " ./gemma -g [filename] -p [filename] -epm [filename] -emu "
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+ cout << " gemma -g [filename] -p [filename] -epm [filename] -emu "
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"[filename] -ebv [filename] -k [filename] -predict [num] -o "
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"[prefix]"
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<< endl;
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cout << " to calculate correlations between SNPs: " << endl;
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- cout << " ./gemma -bfile [prefix] -calccor -o [prefix]" << endl;
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- cout << " ./gemma -g [filename] -p [filename] -calccor -o [prefix]"
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+ cout << " gemma -bfile [prefix] -calccor -o [prefix]" << endl;
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+ cout << " gemma -g [filename] -p [filename] -calccor -o [prefix]"
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<< endl;
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cout << endl;
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}
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@@ -3148,7 +3148,7 @@ void GEMMA::WriteLog(int argc, char **argv, PARAM &cPa
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#ifdef OPENBLAS
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#ifndef OPENBLAS_LEGACY
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- outfile << "## OpenBlas =" << OPENBLAS_VERSION << " - " << openblas_get_config() << endl;
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+ //outfile << "## OpenBlas =" << OPENBLAS_VERSION << " - " << openblas_get_config() << endl;
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outfile << "## arch = " << openblas_get_corename() << endl;
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outfile << "## threads = " << openblas_get_num_threads() << endl;
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#else
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