1 files changed, 49 insertions, 13 deletions
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 467056e..625298e 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -2,11 +2,43 @@
 
 gemma=../bin/gemma
 
+testCenteredRelatednessMatrixKFullLOCO1() {
+    outn=mouse_hs1940_full_LOCO1
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
+           -p ../example/mouse_hs1940.pheno.txt \
+           -a ../example/mouse_hs1940.anno.txt \
+           -loco 1 -gk -debug -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    outfn=output/$outn.cXX.txt
+    assertEquals 0 $?
+    assertEquals "1940" `wc -l < $outfn`
+    assertEquals "2246.57" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
+testUnivariateLinearMixedModelFullLOCO1() {
+    outn=mouse_hs1940_CD8_full_LOCO1_lmm
+    $gemma -g ../example/mouse_hs1940.geno.txt.gz \
+           -p ../example/mouse_hs1940.pheno.txt \
+	   -n 1 \
+	   -loco 1 \
+           -a ../example/mouse_hs1940.anno.txt \
+           -k ./output/mouse_hs1940_full_LOCO1.cXX.txt \
+	   -lmm \
+	   -debug \
+           -o $outn
+    assertEquals 0 $?
+    grep "total computation time" < output/$outn.log.txt
+    assertEquals 0 $?
+    outfn=output/$outn.assoc.txt
+    assertEquals "951" `wc -l < $outfn`
+    assertEquals "267509369.79" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
+}
+
 testCenteredRelatednessMatrixK() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz \
-      -p ../example/mouse_hs1940.pheno.txt \
-      -a ../example/mouse_hs1940.anno.txt \
-      -gk -o mouse_hs1940
+           -p ../example/mouse_hs1940.pheno.txt \
+           -gk -o mouse_hs1940
     assertEquals 0 $?
     grep "total computation time" < output/mouse_hs1940.log.txt
     assertEquals 0 $?
@@ -14,36 +46,40 @@ testCenteredRelatednessMatrixK() {
     assertEquals "1940" `wc -l < $outfn`
     assertEquals "3763600" `wc -w < $outfn`
     assertEquals "0.335" `head -c 5 $outfn`
-    assertEquals "24.9799" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
+    assertEquals "1119.64" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
 }
 
 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
+           -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 0 $?
     grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
     assertEquals 0 $?
     outfn=output/mouse_hs1940_CD8_lmm.assoc.txt
     assertEquals "118459" `wc -w < $outfn`
-    assertEquals "92047" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
+    assertEquals "4038557453.62" `perl -nle 'foreach $x (split(/\s+/,$_)) { $sum += sprintf("%.2f",(substr($x,,0,6))) } END { printf "%.2f",$sum }' $outfn`
 }
 
 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
+           -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
     assertEquals 0 $?
     grep "total computation time" < output/mouse_hs1940_CD8MCH_lmm.log.txt
     assertEquals 0 $?
 
     outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
     assertEquals "139867" `wc -w < $outfn`
-    assertEquals "92079" `perl -nle '$sum += substr($_,0,6) } END { print $sum' $outfn`
+    assertEquals "4029037056.54" `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