diff options
Diffstat (limited to 'test')
| -rwxr-xr-x | test/dev_test_suite.sh | 5 | ||||
| -rwxr-xr-x | test/test_suite.sh | 12 |
2 files changed, 10 insertions, 7 deletions
diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh index 0d3d8a0..ad743ff 100755 --- a/test/dev_test_suite.sh +++ b/test/dev_test_suite.sh @@ -14,6 +14,7 @@ testBXDStandardRelatednessMatrixKSingularError() { -c ../example/BXD_covariates.txt \ -a ../example/BXD_snps.txt \ -gk \ + -no-check \ -o $outn assertEquals 22 $? # should show singular error } @@ -56,7 +57,7 @@ testBXDLMMLikelihoodRatio() { -c ../example/BXD_covariates2.txt \ -a ../example/BXD_snps.txt \ -k ./output/BXD.cXX.txt \ - -lmm 2 -maf 0.1 \ + -lmm 2 -no-check -maf 0.1 \ -o $outn assertEquals 0 $? @@ -89,7 +90,7 @@ testUnivariateLinearMixedModelLOCO1() { -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940_LOCO1.cXX.txt \ -snps ../example/mouse_hs1940_snps.txt -lmm \ - -nind 400 \ + -nind 400 -no-check \ -o $outn assertEquals 0 $? grep "total computation time" < output/$outn.log.txt diff --git a/test/test_suite.sh b/test/test_suite.sh index 7af33aa..faddd43 100755 --- a/test/test_suite.sh +++ b/test/test_suite.sh @@ -8,7 +8,7 @@ testBslmm1() { $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \ -p ../example/mouse_hs1940.pheno.txt \ -n 2 -a ../example/mouse_hs1940.anno.txt \ - -bslmm \ + -bslmm -no-check \ -o $outn -w 1000 -s 10000 -seed 1 assertEquals 0 $? outfn1=output/$outn.hyp.txt @@ -39,7 +39,7 @@ testBslmm3() { -a ../example/mouse_hs1940.anno.txt \ -bslmm \ -o $outn \ - -w 1000 -s 10000 -seed 1 + -w 1000 -s 10000 -seed 1 -no-check assertEquals 0 $? outfn=output/$outn.hyp.txt # assertEquals "291" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.0f",(substr($x,,0,6))) } END { printf "%.0f",100*$sum }' $outfn` @@ -54,7 +54,7 @@ testBslmm4() { -emu ./output/mouse_hs1940_CD8_bslmm.log.txt \ -ebv ./output/mouse_hs1940_CD8_bslmm.bv.txt \ -k ./output/mouse_hs1940_CD8_train.cXX.txt \ - -predict \ + -predict -no-check \ -o $outn assertEquals 0 $? outfn=output/$outn.prdt.txt @@ -98,7 +98,7 @@ testUnivariateLinearMixedModelFullLOCO1() { -loco 1 \ -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940_full_LOCO1.cXX.txt \ - -lmm \ + -lmm -no-check \ -o $outn assertEquals 0 $? grep "total computation time" < output/$outn.log.txt @@ -142,7 +142,8 @@ testLinearMixedModelPhenotypes() { -n 1 6 \ -a ../example/mouse_hs1940.anno.txt \ -k ./output/mouse_hs1940.cXX.txt \ - -lmm -o mouse_hs1940_CD8MCH_lmm + -lmm -no-check \ + -o mouse_hs1940_CD8MCH_lmm assertEquals 0 $? outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt @@ -172,6 +173,7 @@ testPlinkLinearMixedModelCovariates() { -lmm 1 \ -maf 0.1 \ -c $datadir/HLC_covariates.txt \ + -no-check \ -o $testname assertEquals 0 $? outfn=output/$testname.assoc.txt |