Fixed problems with duplicate symbols in io.o, lmm.o, param.o and vc.o; created a Makefile for Mac OS X (tested on 10.11, i.e., El Capitan).

5 files changed, 132 insertions, 71 deletions

diff --git a/Makefile.osx b/Makefile.osx
new file mode 100644
index 0000000..e5d5a26
--- /dev/null
+++ b/Makefile.osx
@@ -0,0 +1,119 @@
+#Makefile
+
+# Supported platforms
+#       Unix / Linux               	LNX
+#       Mac                        	MAC
+# Compilation options
+#       link to LAPACK              WITH_LAPACK
+#       32-bit binary        		FORCE_32BIT
+#       dynamic compilation    		FORCE_DYNAMIC
+#       float precision				FORCE_FLOAT
+
+# Set this variable to either LNX or MAC
+SYS = MAC
+# Leave blank after "=" to disable; put "= 1" to enable
+# Disable WITH_LAPACK option can slow computation speed significantly and is not recommended
+# Disable WITH_ARPACK option only disable -apprx option in the software
+WITH_LAPACK = 1
+FORCE_32BIT = 
+FORCE_DYNAMIC = 1
+FORCE_FLOAT = 
+DIST_NAME = gemma-0.95alpha
+
+# --------------------------------------------------------------------
+# Edit below this line with caution
+# --------------------------------------------------------------------
+BIN_DIR  = ./bin
+
+SRC_DIR  = ./src
+
+CPP = g++
+
+CPPFLAGS = -F /System/Library/Frameworks -Wall -O3 \
+  -I/usr/local/opt/gsl@1/include
+
+LIBS = -lgsl -lgslcblas -lz -L/usr/local/opt/gsl@1/lib
+
+OUTPUT = $(BIN_DIR)/gemma
+
+ifdef FORCE_FLOAT
+OUTPUT = $(BIN_DIR)/gemmaf
+endif
+
+SOURCES = $(SRC_DIR)/main.cpp
+
+HDR = 
+
+# Detailed libary paths, D for dynamic and S for static
+
+LIBS_LNX_D_LAPACK = -llapack
+LIBS_MAC_D_LAPACK = -framework Accelerate
+LIBS_LNX_S_LAPACK = /usr/lib/lapack/liblapack.a -lgfortran  /usr/lib/atlas-base/libatlas.a /usr/lib/libblas/libblas.a -Wl,--allow-multiple-definition 
+
+# Options
+
+ifdef FORCE_FLOAT
+  CPPFLAGS += -DFORCE_FLOAT
+  SOURCES += $(SRC_DIR)/param_float.cpp $(SRC_DIR)/gemma_float.cpp $(SRC_DIR)/io_float.cpp $(SRC_DIR)/lm_float.cpp $(SRC_DIR)/vc_float.cpp $(SRC_DIR)/lmm_float.cpp $(SRC_DIR)/mvlmm_float.cpp $(SRC_DIR)/bslmm_float.cpp $(SRC_DIR)/prdt_float.cpp $(SRC_DIR)/mathfunc_float.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp
+  HDR += $(SRC_DIR)/param_float.h $(SRC_DIR)/gemma_float.h $(SRC_DIR)/io_float.h $(SRC_DIR)/lm_float.h $(SRC_DIR)/lmm_float.h $(SRC_DIR)/vc_float.h $(SRC_DIR)/mvlmm_float.h $(SRC_DIR)/bslmm_float.h $(SRC_DIR)/prdt_float.h $(SRC_DIR)/mathfunc_float.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
+else
+  SOURCES += $(SRC_DIR)/param.cpp $(SRC_DIR)/gemma.cpp $(SRC_DIR)/io.cpp $(SRC_DIR)/lm.cpp $(SRC_DIR)/lmm.cpp $(SRC_DIR)/vc.cpp $(SRC_DIR)/mvlmm.cpp $(SRC_DIR)/bslmm.cpp $(SRC_DIR)/prdt.cpp $(SRC_DIR)/mathfunc.cpp $(SRC_DIR)/gzstream.cpp $(SRC_DIR)/eigenlib.cpp
+  # HDR += $(SRC_DIR)/param.h $(SRC_DIR)/gemma.h $(SRC_DIR)/io.h $(SRC_DIR)/lm.h $(SRC_DIR)/lmm.h $(SRC_DIR)/vc.h $(SRC_DIR)/mvlmm.h $(SRC_DIR)/bslmm.h $(SRC_DIR)/prdt.h $(SRC_DIR)/mathfunc.h $(SRC_DIR)/gzstream.h $(SRC_DIR)/eigenlib.h
+endif
+
+ifdef WITH_LAPACK
+  OBJS += $(SRC_DIR)/lapack.o
+  CPPFLAGS += -DWITH_LAPACK
+ifeq ($(SYS), MAC)
+  LIBS += $(LIBS_MAC_D_LAPACK)
+else
+ifdef FORCE_DYNAMIC
+  LIBS += $(LIBS_LNX_D_LAPACK)
+else
+  LIBS += $(LIBS_LNX_S_LAPACK)
+endif
+endif
+  SOURCES += $(SRC_DIR)/lapack.cpp
+  HDR += $(SRC_DIR)/lapack.h
+endif
+
+ifdef FORCE_32BIT
+  CPPFLAGS += -m32
+else
+  CPPFLAGS += -m64
+endif
+
+ifdef FORCE_DYNAMIC
+else
+  CPPFLAGS += -static
+endif
+
+
+# all
+OBJS = $(SOURCES:.cpp=.o)
+
+all: $(OUTPUT)
+
+$(OUTPUT): $(OBJS)
+	$(CPP) $(CPPFLAGS) $(OBJS) $(LIBS) -o $(OUTPUT)
+
+$(OBJS) : $(HDR)
+
+.cpp.o: 
+	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
+.SUFFIXES : .cpp .c .o $(SUFFIXES)
+
+
+clean:
+	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ ${SRC_DIR}/*_float.* $(OUTPUT)
+
+DIST_COMMON = COPYING.txt README.txt Makefile
+DIST_SUBDIRS = src doc example bin
+
+tar:
+	mkdir -p ./$(DIST_NAME)
+	cp $(DIST_COMMON) ./$(DIST_NAME)/
+	cp -r $(DIST_SUBDIRS) ./$(DIST_NAME)/
+	tar cvzf $(DIST_NAME).tar.gz ./$(DIST_NAME)/
+	rm -r ./$(DIST_NAME)
+
diff --git a/src/io.cpp b/src/io.cpp
index 64eb8e3..fcbbec7 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -47,10 +47,9 @@
 #include "io.h"
 #endif
 
-
 using namespace std;
 
-
+bool ReadHeader_io (const string &line, HEADER &header);
 
 //Print process bar
 void ProgressBar (string str, double p, double total)
@@ -181,7 +180,7 @@ bool ReadFile_snps_header (const string &file_snps, set<string> &setSnps)
 	//read header
 	HEADER header;
 	!safeGetline(infile, line).eof();
-	ReadHeader (line, header);
+	ReadHeader_io (line, header);
 
 	if (header.rs_col==0 && (header.chr_col==0 || header.pos_col==0) ) {
 	  cout<<"missing rs id in the hearder"<<endl;
@@ -2501,7 +2500,7 @@ bool bgenKin (const string &file_oxford, vector<int> &indicator_snp, const int k
 
 
 //read header to determine which column contains which item
-bool ReadHeader (const string &line, HEADER &header)
+bool ReadHeader_io (const string &line, HEADER &header)
 {
   string rs_ptr[]={"rs","RS","snp","SNP","snps","SNPS","snpid","SNPID","rsid","RSID","MarkerName"};
   set<string> rs_set(rs_ptr, rs_ptr+11);
@@ -2636,7 +2635,7 @@ bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, size_
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_io (line, header);
 
   //use the header to count the number of categories
   n_vc=header.coln;
@@ -3209,7 +3208,7 @@ bool ReadFile_wsnp (const string &file_wcat, const size_t n_vc, map<string, vect
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_io (line, header);
 
   while (!safeGetline(infile, line).eof()) {
     if (isBlankLine(line)) {continue;}
@@ -3282,7 +3281,7 @@ void ReadFile_beta (const string &file_beta, const map<string, size_t> &mapRS2ca
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_io (line, header);
 
   if (header.n_col==0 ) {
     if ( (header.nobs_col==0 && header.nmis_col==0) && (header.ncase_col==0 && header.ncontrol_col==0) ) {
@@ -3413,7 +3412,7 @@ void ReadFile_beta (const string &file_beta, const map<string, double> &mapRS2wA
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_io (line, header);
 
   if (header.n_col==0 ) {
     if ( (header.nobs_col==0 && header.nmis_col==0) && (header.ncase_col==0 && header.ncontrol_col==0) ) {
@@ -3846,21 +3845,6 @@ void ReadFile_mstudy (const string &file_mstudy, gsl_matrix *Vq_mat, gsl_vector
   return;
 }
 
-
-//copied from lmm.cpp; is used in the following function compKtoV
-//map a number 1-(n_cvt+2) to an index between 0 and [(n_c+2)^2+(n_c+2)]/2-1
-size_t GetabIndex (const size_t a, const size_t b, const size_t n_cvt) {
-	if (a>n_cvt+2 || b>n_cvt+2 || a<=0 || b<=0) {cout<<"error in GetabIndex."<<endl; return 0;}
-	size_t index;
-	size_t l, h;
-	if (b>a) {l=a; h=b;} else {l=b; h=a;}
-
-	size_t n=n_cvt+2;
-	index=(2*n-l+2)*(l-1)/2+h-l;
-
-	return index;
-}
-
 //read reference file
 void ReadFile_mref (const string &file_mref, gsl_matrix *S_mat, gsl_matrix *Svar_mat, gsl_vector *s_vec, size_t &ni)
 {
diff --git a/src/lmm.cpp b/src/lmm.cpp
index 044f33c..a707534 100644
--- a/src/lmm.cpp
+++ b/src/lmm.cpp
@@ -183,30 +183,6 @@ void LMM::WriteFiles ()
 	return;
 }
 
-
-
-
-
-
-
-
-
-
-
-//map a number 1-(n_cvt+2) to an index between 0 and [(n_c+2)^2+(n_c+2)]/2-1
-size_t GetabIndex (const size_t a, const size_t b, const size_t n_cvt) {
-	if (a>n_cvt+2 || b>n_cvt+2 || a<=0 || b<=0) {cout<<"error in GetabIndex."<<endl; return 0;}
-	size_t index;
-	size_t l, h;
-	if (b>a) {l=a; h=b;} else {l=b; h=a;}
-
-	size_t n=n_cvt+2;
-	index=(2*n-l+2)*(l-1)/2+h-l;
-
-	return index;
-}
-
-
 void CalcPab (const size_t n_cvt, const size_t e_mode, const gsl_vector *Hi_eval, const gsl_matrix *Uab, const gsl_vector *ab, gsl_matrix *Pab)
 {
 	size_t index_ab, index_aw, index_bw, index_ww;
diff --git a/src/param.h b/src/param.h
index 4b4ad29..8db3590 100644
--- a/src/param.h
+++ b/src/param.h
@@ -299,6 +299,7 @@ public:
 	void UpdateSNP (const map<string, double> &mapRS2wA);
 };
 
-
+size_t GetabIndex (const size_t a, const size_t b, const size_t n_cvt);
+  
 #endif
 
diff --git a/src/vc.cpp b/src/vc.cpp
index 94bf931..f17a9e9 100644
--- a/src/vc.cpp
+++ b/src/vc.cpp
@@ -453,7 +453,7 @@ int LogRL_dev12 (const gsl_vector *log_sigma2, void *params, gsl_vector *dev1, g
 
 
 //read header to determine which column contains which item
-bool ReadHeader (const string &line, HEADER &header)
+bool ReadHeader_vc (const string &line, HEADER &header)
 {
   string rs_ptr[]={"rs","RS","snp","SNP","snps","SNPS","snpid","SNPID","rsid","RSID"};
   set<string> rs_set(rs_ptr, rs_ptr+10);
@@ -586,7 +586,7 @@ void ReadFile_cor (const string &file_cor, const set<string> &setSnps, vector<st
 
   //header
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_vc (line, header);
 
   if (header.n_col==0 ) {
     if (header.nobs_col==0 && header.nmis_col==0) {
@@ -700,7 +700,7 @@ void ReadFile_beta (const bool flag_priorscale, const string &file_beta, const m
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_vc (line, header);
 
   if (header.n_col==0 ) {
     if (header.nobs_col==0 && header.nmis_col==0) {
@@ -869,7 +869,7 @@ void ReadFile_cor (const string &file_cor, const vector<string> &vec_rs, const v
   HEADER header;
 
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_vc (line, header);
 
   while (!safeGetline(infile, line).eof()) {
     //do not read cor values this time; upto col_n-1
@@ -1059,25 +1059,6 @@ void ReadFile_cor (const string &file_cor, const vector<string> &vec_rs, const v
   return;
 }
 
-
-
-
-
-//copied from lmm.cpp; is used in the following function VCss
-//map a number 1-(n_cvt+2) to an index between 0 and [(n_c+2)^2+(n_c+2)]/2-1
-size_t GetabIndex (const size_t a, const size_t b, const size_t n_cvt) {
-	if (a>n_cvt+2 || b>n_cvt+2 || a<=0 || b<=0) {cout<<"error in GetabIndex."<<endl; return 0;}
-	size_t index;
-	size_t l, h;
-	if (b>a) {l=a; h=b;} else {l=b; h=a;}
-
-	size_t n=n_cvt+2;
-	index=(2*n-l+2)*(l-1)/2+h-l;
-
-	return index;
-}
-
-
 //use the new method to calculate variance components with summary statistics
 //first, use a function CalcS to compute S matrix (where the diagonal elements are part of V(q) ), and then use bootstrap to compute the variance for S, use a set of genotypes, phenotypes, and individual ids, and snp category label
 void CalcVCss(const gsl_matrix *Vq, const gsl_matrix *S_mat, const gsl_matrix *Svar_mat, const gsl_vector *q_vec, const gsl_vector *s_vec, const double df, vector<double> &v_pve, vector<double> &v_se_pve, double &pve_total, double &se_pve_total, vector<double> &v_sigma2, vector<double> &v_se_sigma2, vector<double> &v_enrich, vector<double> &v_se_enrich) {