1 files changed, 68 insertions, 11 deletions

diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 0fc4423..0d3d8a0 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -1,29 +1,31 @@
 #!/usr/bin/env bash
 
 gemma=../bin/gemma
+# gemmaopts="-debug -strict"
+gemmaopts="-debug"
 
 # Related to https://github.com/genetics-statistics/GEMMA/issues/78
 testBXDStandardRelatednessMatrixKSingularError() {
     outn=BXDerr
     rm -f output/$outn.*
-    $gemma -g ../example/BXD_geno.txt.gz \
+    $gemma $gemmaopts \
+           -g ../example/BXD_geno.txt.gz \
            -p ../example/BXD_pheno.txt \
            -c ../example/BXD_covariates.txt \
            -a ../example/BXD_snps.txt \
            -gk \
-           -debug -o $outn
+           -o $outn
     assertEquals 22 $? # should show singular error
 }
 
 testBXDStandardRelatednessMatrixK() {
     outn=BXD
     rm -f output/$outn.*
-    $gemma -g ../example/BXD_geno.txt.gz \
+    $gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
            -p ../example/BXD_pheno.txt \
            -c ../example/BXD_covariates2.txt \
            -a ../example/BXD_snps.txt \
            -gk \
-           -debug \
            -o $outn
     assertEquals 0 $?
     outfn=output/$outn.cXX.txt
@@ -31,28 +33,43 @@ testBXDStandardRelatednessMatrixK() {
     assertEquals "-116.11" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
 }
 
+testBXDLMLikelihoodRatio() {
+    outn=BXD_LM_LR
+    $gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
+           -p ../example/BXD_pheno.txt \
+           -c ../example/BXD_covariates2.txt \
+           -a ../example/BXD_snps.txt \
+           -k ./output/BXD.cXX.txt \
+           -lm 4 -maf 0.1 \
+           -o $outn
+    assertEquals 0 $?
+
+    outfn=output/$outn.assoc.txt
+    assertEquals "95134" `wc -w < $outfn`
+    assertEquals "3089042886.28" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
 testBXDLMMLikelihoodRatio() {
     outn=BXD_LMM_LR
-    $gemma -g ../example/BXD_geno.txt.gz \
+    $gemma $gemmaopts -g ../example/BXD_geno.txt.gz \
            -p ../example/BXD_pheno.txt \
            -c ../example/BXD_covariates2.txt \
            -a ../example/BXD_snps.txt \
            -k ./output/BXD.cXX.txt \
            -lmm 2 -maf 0.1 \
-           -debug \
            -o $outn
     assertEquals 0 $?
 
     outfn=output/$outn.assoc.txt
-    assertEquals "80498" `wc -w < $outfn`
+    assertEquals "73180" `wc -w < $outfn`
     assertEquals "3088458212.93" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
 }
 
 testCenteredRelatednessMatrixKLOCO1() {
     outn=mouse_hs1940_LOCO1
     rm -f output/$outn.*
-    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
-           -a ../example/mouse_hs1940.anno.txt -snps ../example/mouse_hs1940_snps.txt -nind 400 -loco 1 -gk -debug -o $outn
+    $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+           -a ../example/mouse_hs1940.anno.txt -snps ../example/mouse_hs1940_snps.txt -nind 400 -loco 1 -gk -o $outn
     assertEquals 0 $?
     grep "total computation time" < output/$outn.log.txt
     outfn=output/$outn.cXX.txt
@@ -65,7 +82,7 @@ testCenteredRelatednessMatrixKLOCO1() {
 testUnivariateLinearMixedModelLOCO1() {
     outn=mouse_hs1940_CD8_LOCO1_lmm
     rm -f output/$outn.*
-    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
+    $gemma $gemmaopts -g ../example/mouse_hs1940.geno.txt.gz \
            -p ../example/mouse_hs1940.pheno.txt \
 	   -n 1 \
 	   -loco 1 \
@@ -73,7 +90,47 @@ testUnivariateLinearMixedModelLOCO1() {
            -k ./output/mouse_hs1940_LOCO1.cXX.txt \
 	   -snps ../example/mouse_hs1940_snps.txt -lmm \
 	   -nind 400 \
-	   -debug \
+           -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    assertEquals 0 $?
+    outfn=output/$outn.assoc.txt
+    assertEquals "68" `wc -l < $outfn`
+    assertEquals "15465346.22" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+testPlinkCenteredRelatednessMatrixKLOCO1() {
+    return 0
+    outn=mouse_hs1940_Plink_LOCO1
+    rm -f output/$outn.*
+    $gemma $gemmaopts -bfile ../example/mouse_hs1940 \
+           -a ../example/mouse_hs1940.anno.txt \
+           -snps ../example/mouse_hs1940_snps.txt \
+           -nind 400 \
+           -loco 1 \
+           -gk \
+           -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    outfn=output/$outn.cXX.txt
+    assertEquals 0 $?
+    assertEquals "400" `wc -l < $outfn`
+    assertEquals "0.312" `head -c 5 $outfn`
+    assertEquals "71.03" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+
+testPlinkUnivariateLinearMixedModelLOCO1() {
+    return 0
+    outn=mouse_hs1940_CD8_Plink_LOCO1_lmm
+    rm -f output/$outn.*
+    $gemma $gemmaopts -bfile ../example/mouse_hs1940 \
+	   -n 1 \
+	   -loco 1 \
+           -k ./output/mouse_hs1940_Plink_LOCO1.cXX.txt \
+           -a ../example/mouse_hs1940.anno.txt \
+	   -snps ../example/mouse_hs1940_snps.txt -lmm \
+	   -nind 400 \
            -o $outn
     assertEquals 0 $?
     grep "total computation time" < output/$outn.log.txt