Putatively fixed -Wc++11-narrowing error in io.cpp (see Issue #24).

3 files changed, 12 insertions, 11 deletions

diff --git a/Makefile.osx b/Makefile.osx
index efa2e4c..8fcab7b 100644
--- a/Makefile.osx
+++ b/Makefile.osx
@@ -30,7 +30,7 @@ SRC_DIR  = ./src
 CPP = g++
 
 CPPFLAGS = -F /System/Library/Frameworks -Wall -O3 \
-  -I/usr/local/opt/gsl@1/include
+  -I/usr/local/opt/gsl@1/include -Wc++11-narrowing
 
 LIBS = /usr/local/opt/gsl@1/lib/libgsl.a \
        /usr/local/opt/gsl@1/lib/libgslcblas.a -lz
diff --git a/example/demo.txt b/example/demo.txt
index 766d949..3231ddc 100644
--- a/example/demo.txt
+++ b/example/demo.txt
@@ -1,13 +1,10 @@
-## Detailed description of the data set is available in the online GEMMA user manual
-## Each of the following steps may take over one minute to run
-
-
-
-
-
+## Detailed description of the data set is available in the online
+## GEMMA user manual. Each of the following steps may take over one
+## minute to run.
 
 ## To calculate a centered relatedness matrix:
-../bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt -a mouse_hs1940.anno.txt -gk -o mouse_hs1940
+../bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \
+  -a mouse_hs1940.anno.txt -gk -o mouse_hs1940
 
 # The estimated relatedness matrix should look like this:
 0.3350590  -0.0227226  0.0103535 ...
@@ -55,7 +52,9 @@ se(pve) in the null model = 0.032774
 ## To perform association tests with a multivariate linear mixed model, for two phenotypes CD8 (column 1) and MCH (column 6):
 ## Notice that the number of individuals in this analysis is different from that above, so the allele frequencies are different between the two analyses
 
-../bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt -n 1 6 -a mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm -o mouse_hs1940_CD8MCH_lmm
+../bin/gemma -g mouse_hs1940.geno.txt.gz -p mouse_hs1940.pheno.txt \
+  -n 1 6 -a mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
+  -lmm -o mouse_hs1940_CD8MCH_lmm
 
 # The result for top 5 SNPs should look like this:
 chr	rs	ps	n_miss	allele1	allele0	af	beta_1	beta_2	Vbeta_1_1	Vbeta_1_2	Vbeta_2_2	p_wald
diff --git a/src/io.cpp b/src/io.cpp
index 4da1590..ccaec30 100644
--- a/src/io.cpp
+++ b/src/io.cpp
@@ -2160,7 +2160,9 @@ bool ReadFile_bgen(const string &file_bgen, const set<string> &setSnps, const gs
 		uint16_t unzipped_data[3*bgen_N];
 
 		if (setSnps.size()!=0 && setSnps.count(rs)==0) {
-		  SNPINFO sInfo={"-9", rs, -9, -9, minor, major, -9, -9, (long int) -9};
+		  SNPINFO sInfo={"-9", rs, -9, -9, minor, major,
+				 static_cast<size_t>(-9), -9, (long int) -9};
+		  
 			snpInfo.push_back(sInfo);
 			indicator_snp.push_back(0);
 			if(CompressedSNPBlocks)