From 0792aee7269e4bf1c2903267e17a12dfebd14884 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 9 Jul 2017 08:33:41 +0000
Subject: Tests: added test for univariate and multivariate LMM

Also added 'make check' command in Makefile and documented in INSTALL.md
---
 .gitignore         |  4 +++-
 INSTALL.md         |  4 ++++
 Makefile           |  2 ++
 test/test_suite.sh | 17 +++++++++++++++++
 4 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 108e607..d6c227e 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,9 +2,11 @@
 *.tar.gz
 src/Eigen
 example/output
+test/output
+./output
 doc/manual.aux
 doc/manual.bbl
 doc/manual.blg
 doc/manual.log
 doc/manual.out
-doc/manual.toc
\ No newline at end of file
+doc/manual.toc
diff --git a/INSTALL.md b/INSTALL.md
index f6eb0c0..32d37f3 100644
--- a/INSTALL.md
+++ b/INSTALL.md
@@ -48,3 +48,7 @@ if you get an Eigen error you may need to override the include
 path. E.g. on GNU Guix with shared libs this may work
 
     make EIGEN_INCLUDE_PATH=~/.guix-profile/include/eigen3 FORCE_DYNAMIC=1
+
+to run GEMMA tests
+
+    make check
diff --git a/Makefile b/Makefile
index 0f25d88..a15c043 100644
--- a/Makefile
+++ b/Makefile
@@ -95,6 +95,8 @@ $(OBJS) : $(HDR)
 	$(CPP) $(CPPFLAGS) $(HEADERS) -c $*.cpp -o $*.o
 .SUFFIXES : .cpp .c .o $(SUFFIXES)
 
+check:
+	./run_tests.sh
 
 clean:
 	rm -rf ${SRC_DIR}/*.o ${SRC_DIR}/*~ *~ $(OUTPUT)
diff --git a/test/test_suite.sh b/test/test_suite.sh
index effc056..8adc5c9 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -11,6 +11,23 @@ testCenteredRelatednessMatrixK() {
     assertEquals "29.691" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940.cXX.txt`
 }
 
+testUnivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt -n 1 \
+           -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt -lmm \
+           -o mouse_hs1940_CD8_lmm
+    assertEquals "118459" `wc -w < output/mouse_hs1940_CD8_lmm.assoc.txt`
+    assertEquals "92047" `awk '{s+=substr($1,0,6)}END{print s}' output/mouse_hs1940_CD8_lmm.assoc.txt`
+}
+
+testMultivariateLinearMixedModel() {
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -n 1 6 -a ../example/mouse_hs1940.anno.txt -k ./output/mouse_hs1940.cXX.txt \
+           -lmm -o mouse_hs1940_CD8MCH_lmm
+    outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
+    assertEquals "139867" `wc -w < $outfn`
+    assertEquals "92079" `awk '{s+=substr($1,0,6)}END{print s}' $outfn`
+}
+
 shunit2=`which shunit2`
 if [ -x "$shunit2" ]; then
     . $shunit2
-- 
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