diff options
| -rw-r--r-- | .gitignore | 4 | ||||
| -rw-r--r-- | INSTALL.md | 4 | ||||
| -rw-r--r-- | Makefile | 2 | ||||
| -rwxr-xr-x | test/test_suite.sh | 17 |
4 files changed, 26 insertions, 1 deletions
@@ -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 @@ -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 @@ -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 |