CoCalc -- patch-src

GitHub Repository: freebsd/freebsd-ports-gnome
Path: blob/main/biology/gemma/files/patch-src_gemma.cpp
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--- 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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