From 12d2acb8f8ea39da448c94754a708c0dd4369c34 Mon Sep 17 00:00:00 2001
From: Peter Carbonetto
Date: Thu, 4 May 2017 15:17:47 -0500
Subject: Fixed problems with duplicate symbols; now using static gsl libraries
 in Makefile.osx so that others don't have to download it using Homebrew.

---
 src/vc.cpp | 27 ++++-----------------------
 1 file changed, 4 insertions(+), 23 deletions(-)

(limited to 'src/vc.cpp')

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) {
-- 
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