Fixed problems with duplicate symbols; now using static gsl libraries in Makefile.osx so that others don't have to download it using Homebrew.

6 files changed, 15 insertions, 73 deletions

diff --git a/src/bslmmdap.cpp b/src/bslmmdap.cpp
index 0bf0e7b..f6e9e9c 100644
--- a/src/bslmmdap.cpp
+++ b/src/bslmmdap.cpp
@@ -42,6 +42,7 @@
 
 #include "logistic.h"
 #include "lapack.h"
+#include "io.h"
 
 #ifdef FORCE_FLOAT
 #include "param_float.h"
@@ -221,7 +222,7 @@ void ReadFile_cat (const string &file_cat, const vector<string> &vec_rs, gsl_mat
   //read header
   HEADER header;
   !safeGetline(infile, line).eof();
-  ReadHeader (line, header);
+  ReadHeader_io (line, header);
 
   //use the header to determine the number of categories
   kc=header.catc_col.size(); kd=header.catd_col.size();
diff --git a/src/io.cpp b/src/io.cpp
index 97b29b0..4da1590 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -50,8 +50,6 @@
 
 using namespace std;
 
-
-
 //Print process bar
 void ProgressBar (string str, double p, double total)
 {
@@ -181,7 +179,7 @@ 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 +2499,7 @@ 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);
@@ -2645,7 +2643,7 @@ 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;
@@ -2746,7 +2744,7 @@ bool ReadFile_catc (const string &file_cat, map<string, vector<double> > &mapRS2
   //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_cat=header.coln;
@@ -3330,7 +3328,7 @@ 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;}
@@ -3403,7 +3401,7 @@ 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) ) {
@@ -3534,7 +3532,7 @@ 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) ) {
@@ -3966,21 +3964,6 @@ 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/io.h b/src/io.h
index c1b762d..073812c 100644
--- a/src/io.h
+++ b/src/io.h
@@ -79,7 +79,7 @@ bool CountFileLines (const string &file_input, size_t &n_lines);
 
 bool ReadFile_gene (const string &file_gene, vector<double> &vec_read, vector<SNPINFO> &snpInfo, size_t &ng_total);
 
-bool ReadHeader (const string &line, HEADER &header);
+bool ReadHeader_io (const string &line, HEADER &header);
 bool ReadFile_cat (const string &file_cat, map<string, size_t> &mapRS2cat, size_t &n_vc);
 bool ReadFile_mcat (const string &file_mcat, map<string, size_t> &mapRS2cat, size_t &n_vc);
 
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 6cb0d97..72b7d85 100644
--- a/src/param.h
+++ b/src/param.h
@@ -307,6 +307,7 @@ 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 c0aa40d..1e0c562 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) {