diff options
Diffstat (limited to 'test/test_suite.sh')
| -rwxr-xr-x | test/test_suite.sh | 31 |
1 files changed, 31 insertions, 0 deletions
diff --git a/test/test_suite.sh b/test/test_suite.sh index 625298e..71901d7 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -80,6 +80,37 @@ testMultivariateLinearMixedModel() { assertEquals "139867" `wc -w < $outfn` assertEquals "4029037056.54" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` } + +testPlinkStandardRelatednessMatrixK() { + testname=testPlinkStandardRelatednessMatrixK + datadir=../example + outfn=output/$testname.sXX.txt + rm -f $outfn + $gemma -bfile $datadir/HLC \ + -gk 2 -o $testname + assertEquals 0 $? + assertEquals 0 $? + assertEquals "427" `wc -l < $outfn` + assertEquals "-358.07" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + +# Test for https://github.com/genetics-statistics/GEMMA/issues/58 +# fixed GSLv2 NaN's that appeared with covariates. +testPlinkMultivariateLinearMixedModel() { + testname=testPlinkMultivariateLinearMixedModel + datadir=../example + $gemma -bfile $datadir/HLC \ + -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \ + -lmm 1 \ + -maf 0.1 \ + -c $datadir/HLC_covariates.txt \ + -o $testname + assertEquals 0 $? + outfn=output/$testname.assoc.txt + assertEquals "223243" `wc -l < $outfn` + assertEquals "89756559859.06" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn` +} + shunit2=`which shunit2` if [ -x "$shunit2" ]; then |