Merge branch 'master' of github.com:genetics-statistics/GEMMA

16 files changed, 20 insertions, 17 deletions

diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp
index e9900e3..6220bb5 100644
--- a/src/bslmmdap.cpp
+++ b/src/bslmmdap.cpp
@@ -39,7 +39,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "bslmmdap.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lm.h"
 #include "lmm.h"
diff --git a/src/gemma.cpp b/src/gemma.cpp
index 97e947a..758aa24 100644
--- a/src/gemma.cpp
+++ b/src/gemma.cpp
@@ -49,7 +49,7 @@ extern "C" {
 #include "bslmm.h"
 #include "bslmmdap.h"
 #include "gemma.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "ldr.h"
 #include "lm.h"
diff --git a/src/io.cpp b/src/gemma_io.cpp
index 923eb11..818c5e8 100644
--- a/src/io.cpp
+++ b/src/gemma_io.cpp
@@ -45,7 +45,7 @@
 // #include "eigenlib.h"
 #include "fastblas.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 
diff --git a/src/io.h b/src/gemma_io.h
index dd1d5c0..dd1d5c0 100644
--- a/src/io.h
+++ b/src/gemma_io.h
diff --git a/src/lm.h b/src/lm.h
index 030e6f9..bcec0ab 100644
--- a/src/lm.h
+++ b/src/lm.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 5822275..acd9667 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -43,7 +43,7 @@
 // #include "eigenlib.h"
 
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "fastblas.h"
 #include "lapack.h"
 #include "lmm.h"
diff --git a/src/lmm.h b/src/lmm.h
index e9740d5..f603599 100644
--- a/src/lmm.h
+++ b/src/lmm.h
@@ -23,7 +23,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 #include <functional>
 #include <tuple>
diff --git a/src/main.cpp b/src/main.cpp
index 706ac35..deadc63 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -58,7 +58,11 @@ int main(int argc, char *argv[]) {
 
   ifstream check_dir((cPar.path_out).c_str());
   if (!check_dir) {
-    mkdir((cPar.path_out).c_str(), S_IRWXU | S_IRGRP | S_IROTH);
+    #ifdef WINDOWS
+      mkdir((cPar.path_out).c_str());
+    #else
+      mkdir((cPar.path_out).c_str(), S_IRWXU | S_IRGRP | S_IROTH);
+    #endif
   }
 
   if (!is_quiet_mode())
diff --git a/src/mvlmm.cpp b/src/mvlmm.cpp
index eee562d..14f8b4a 100644
--- a/src/mvlmm.cpp
+++ b/src/mvlmm.cpp
@@ -39,7 +39,7 @@
 
 #include "fastblas.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lmm.h"
 #include "mvlmm.h"
diff --git a/src/mvlmm.h b/src/mvlmm.h
index 4329ad1..b92bd5e 100644
--- a/src/mvlmm.h
+++ b/src/mvlmm.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/param.cpp b/src/param.cpp
index bf6c195..edee79d 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -35,7 +35,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "eigenlib.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "mathfunc.h"
 #include "param.h"
 
@@ -521,7 +521,7 @@ void PARAM::CheckParam(void) {
       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;
+         << "-calccov is specified correctly." << endl;
     error = true;
   }
   if (miss_level > 1) {
diff --git a/src/prdt.cpp b/src/prdt.cpp
index fc0abe8..42912a8 100644
--- a/src/prdt.cpp
+++ b/src/prdt.cpp
@@ -32,8 +32,7 @@
 #include <vector>
 
 #include "gzstream.h"
-#include "io.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 #include "prdt.h"
diff --git a/src/varcov.cpp b/src/varcov.cpp
index e9c7295..055d3b1 100644
--- a/src/varcov.cpp
+++ b/src/varcov.cpp
@@ -37,7 +37,7 @@
 #include "gsl/gsl_vector.h"
 
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "mathfunc.h"
 #include "param.h"
diff --git a/src/varcov.h b/src/varcov.h
index 47b4f9d..fa707d5 100644
--- a/src/varcov.h
+++ b/src/varcov.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;
diff --git a/src/vc.cpp b/src/vc.cpp
index 1a16c07..416a3e4 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -45,7 +45,7 @@
 
 #include "eigenlib.h"
 #include "gzstream.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "lapack.h"
 #include "lmm.h"
 #include "mathfunc.h"
diff --git a/src/vc.h b/src/vc.h
index 49397bb..3586433 100644
--- a/src/vc.h
+++ b/src/vc.h
@@ -21,7 +21,7 @@
 
 #include "gsl/gsl_matrix.h"
 #include "gsl/gsl_vector.h"
-#include "io.h"
+#include "gemma_io.h"
 #include "param.h"
 
 using namespace std;