Adding debug statements on entering functions and added test for issue 58

2 files changed, 35 insertions, 7 deletions

diff --git a/test/dev_test_suite.sh b/test/dev_test_suite.sh
index 9e49251..2bd432e 100755
--- a/test/dev_test_suite.sh
+++ b/test/dev_test_suite.sh
@@ -2,7 +2,6 @@
 
 gemma=../bin/gemma
 
-
 # Related to https://github.com/genetics-statistics/GEMMA/issues/78
 testBXDStandardRelatednessMatrixKSingularError() {
     outn=BXDerr
@@ -65,10 +64,12 @@ testCenteredRelatednessMatrixKLOCO1() {
 testUnivariateLinearMixedModelLOCO1() {
     outn=mouse_hs1940_CD8_LOCO1_lmm
     rm -f output/$outn.*
-    $gemma -g ../example/mouse_hs1940.geno.txt.gz -p ../example/mouse_hs1940.pheno.txt \
+    $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_LOCO1.cXX.txt \
+           -a ../example/mouse_hs1940.anno.txt \
+           -k ./output/mouse_hs1940_LOCO1.cXX.txt \
 	   -snps ../example/mouse_hs1940_snps.txt -lmm \
 	   -nind 400 \
 	   -debug \
diff --git a/test/test_suite.sh b/test/test_suite.sh
index 44eb14c..fa66b7a 100755
--- a/test/test_suite.sh
+++ b/test/test_suite.sh
@@ -36,7 +36,7 @@ testUnivariateLinearMixedModelFullLOCO1() {
 testCenteredRelatednessMatrixK() {
     $gemma -g ../example/mouse_hs1940.geno.txt.gz \
            -p ../example/mouse_hs1940.pheno.txt \
-           -gk -o mouse_hs1940
+           -gk -o mouse_hs1940 -debug
     assertEquals 0 $?
     outfn=output/mouse_hs1940.cXX.txt
     assertEquals "1940" `wc -l < $outfn`
@@ -52,7 +52,8 @@ testUnivariateLinearMixedModel() {
            -a ../example/mouse_hs1940.anno.txt \
            -k ./output/mouse_hs1940.cXX.txt \
            -lmm \
-           -o mouse_hs1940_CD8_lmm
+           -o mouse_hs1940_CD8_lmm \
+           -debug
     assertEquals 0 $?
     grep "total computation time" < output/mouse_hs1940_CD8_lmm.log.txt
     assertEquals 0 $?
@@ -67,7 +68,8 @@ testMultivariateLinearMixedModel() {
            -n 1 6 \
            -a ../example/mouse_hs1940.anno.txt \
            -k ./output/mouse_hs1940.cXX.txt \
-           -lmm -o mouse_hs1940_CD8MCH_lmm
+           -lmm -o mouse_hs1940_CD8MCH_lmm \
+           -debug
     assertEquals 0 $?
 
     outfn=output/mouse_hs1940_CD8MCH_lmm.assoc.txt
@@ -81,7 +83,8 @@ testPlinkStandardRelatednessMatrixK() {
     outfn=output/$testname.sXX.txt
     rm -f $outfn
     $gemma -bfile $datadir/HLC \
-           -gk 2 -o $testname
+           -gk 2 -o $testname \
+           -debug
     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`
@@ -97,6 +100,30 @@ testPlinkMultivariateLinearMixedModel() {
            -lmm 1 \
            -maf 0.1 \
            -c $datadir/HLC_covariates.txt \
+           -debug \
+           -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`
+}
+
+testPlinkMultivariateLinearMixedModelMultiplePhenotypes_Issue58() {
+    # n=2 is original pheno in fam file
+    # n=1 is causal1
+    # n=3..12 is causal2
+    # n=13..22 is causal3
+    # -n 1 2 3 15 is independent
+    testname=testPlinkMultivariateLinearMixedModelMultiplePhenotypes
+    datadir=../example
+    $gemma -bfile $datadir/HLC \
+           -p $datadir/HLC.simu.pheno.txt \
+           -k output/testPlinkStandardRelatednessMatrixK.sXX.txt \
+           -lmm 1 \
+           -maf 0.1 \
+           -n 1 2 3 15 \
+           -c $datadir/HLC_covariates.txt \
+           -debug \
            -o $testname
     assertEquals 0 $?
     outfn=output/$testname.assoc.txt