From b9758364059d52e153a9f1b4fcae3bc3f3e68422 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 7 Jul 2017 06:54:26 +0000
Subject: Fix spacing
---
src/param.cpp | 24 ++++++++++++------------
1 file changed, 12 insertions(+), 12 deletions(-)
(limited to 'src/param.cpp')
diff --git a/src/param.cpp b/src/param.cpp
index a56f5eb..413d517 100644
--- a/src/param.cpp
+++ b/src/param.cpp
@@ -66,7 +66,7 @@ time_UtZ(0.0), time_opt(0.0), time_Omega(0.0)
// Read files: obtain ns_total, ng_total, ns_test, ni_test.
void PARAM::ReadFiles (void) {
string file_str;
-
+
// Read cat file.
if (!file_mcat.empty()) {
if (ReadFile_mcat (file_mcat, mapRS2cat, n_vc)==false) {error=true;}
@@ -216,7 +216,7 @@ void PARAM::ReadFiles (void) {
// If both fam file and pheno files are used, use
// phenotypes inside the pheno file.
if (!file_pheno.empty()) {
-
+
// Phenotype file before genotype file.
if (ReadFile_pheno (file_pheno, indicator_pheno, pheno,
p_column)==false) {error=true;}
@@ -247,7 +247,7 @@ void PARAM::ReadFiles (void) {
// Read genotype and phenotype file for BIMBAM format.
if (!file_geno.empty()) {
-
+
// Annotation file before genotype file.
if (!file_anno.empty() ) {
if (ReadFile_anno (file_anno, mapRS2chr, mapRS2bp,
@@ -297,11 +297,11 @@ void PARAM::ReadFiles (void) {
if (ReadFile_bim (file_str, snpInfo)==false) {error=true;}
if (t==0) {
-
+
// If both fam file and pheno files are used, use
// phenotypes inside the pheno file.
if (!file_pheno.empty()) {
-
+
// Phenotype file before genotype file.
if (ReadFile_pheno (file_pheno, indicator_pheno, pheno,
p_column)==false) {
@@ -347,7 +347,7 @@ void PARAM::ReadFiles (void) {
// Read genotype and phenotype file for multiple BIMBAM files.
if (!file_mgeno.empty()) {
-
+
// Annotation file before genotype file.
if (!file_anno.empty() ) {
if (ReadFile_anno (file_anno, mapRS2chr, mapRS2bp,
@@ -788,7 +788,7 @@ void PARAM::CheckParam (void) {
if (!file_bfile.empty()) {flag++;}
if (!file_geno.empty()) {flag++;}
if (!file_gene.empty()) {flag++;}
-
+
// WJA added.
if (!file_oxford.empty()) {flag++;}
@@ -982,7 +982,7 @@ void PARAM::CheckData (void) {
// WJA NOTE: I added this condition so that covariates can be added
// through sample, probably not exactly what is wanted.
- if(file_oxford.empty())
+ if(file_oxford.empty())
{
if ((file_cvt).empty() || (indicator_cvt).size()==0) {
n_cvt=1;
@@ -1017,7 +1017,7 @@ void PARAM::CheckData (void) {
"the number of individuals. "<<endl;
return;
}
-
+
if ( (indicator_read).size()!=0 &&
(indicator_read).size()!=(indicator_idv).size()) {
error=true;
@@ -1025,7 +1025,7 @@ void PARAM::CheckData (void) {
"match the number of individuals. "<<endl;
return;
}
-
+
// Calculate ni_total and ni_test, and set indicator_idv to 0
// whenever indicator_cvt=0, and calculate np_obs and np_miss.
ni_total=(indicator_idv).size();
@@ -1896,7 +1896,7 @@ void PARAM::CheckCvt () {
// Post-process phentoypes and covariates.
void PARAM::ProcessCvtPhen () {
-
+
// Convert indicator_pheno to indicator_idv.
int k=1;
indicator_idv.clear();
@@ -1949,7 +1949,7 @@ void PARAM::ProcessCvtPhen () {
cout<<"error! number of subsamples is less than number of"<<
"analyzed individuals. "<<endl;
} else {
-
+
// Set up random environment.
gsl_rng_env_setup();
gsl_rng *gsl_r;
--
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