1 files changed, 32 insertions, 5 deletions
diff --git a/test/test-uvlmm-integration.scm b/test/test-uvlmm-integration.scm
index 97539b8..10af32f 100755..100644
--- a/test/test-uvlmm-integration.scm
+++ b/test/test-uvlmm-integration.scm
@@ -11,13 +11,38 @@ exec guile --debug -s "$0" "$@"
   #:use-module (ice-9 rdelim)
   )
 
-(test-begin "external-gemma-run")
+(define kinship-fn "./output/mouse_hs1940.cXX.txt")
+(define gwa-fn "./output/mouse_hs1940.assoc.txt")
 
-(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -gk -o mouse_hs1940 -debug"))]
+(test-begin "uvlmm-mdb-kinship-run")
+
+(when (file-exists? kinship-fn)
+  (delete-file kinship-fn))
+(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.mdb -p ./example/mouse_hs1940.pheno.txt -gk -o mouse_hs1940 -debug"))]
   (test-eqv 0 err))
-(let [(err (system "./build/bin/Debug/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 -o mouse_hs1940 -lmm 9 -debug"))]
+
+(test-end "uvlmm-mdb-kinship-run")
+
+#!
+(test-begin "uvlmm-bimbam-kinship-run")
+
+(when (file-exists? kinship-fn)
+  (delete-file kinship-fn))
+(let [(err (system "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -gk -p ./example/mouse_hs1940.pheno.txt -o mouse_hs1940 -debug"))]
   (test-eqv 0 err))
-(call-with-input-file "output/mouse_hs1940.assoc.txt"
+
+(test-end "uvlmm-bimbam-kinship-run")
+
+
+(test-begin "uvlmm-bimbam-gwa-run")
+
+(when (file-exists? gwa-fn)
+  (delete-file gwa-fn))
+;; The following integration test runs gemma uvlmm and adds up the output column as a check.
+;; It uses the kinship-run matrix from the earlier test
+(let [(err (system (string-append "./build/bin/Debug/gemma -g ./example/mouse_hs1940.geno.txt.gz -p ./example/mouse_hs1940.pheno.txt -n 1 -a ./example/mouse_hs1940.anno.txt -k " kinship-fn " -o mouse_hs1940 -lmm 9 -debug")))]
+  (test-eqv 0 err))
+(call-with-input-file gwa-fn
   (lambda (port)
     (read-line port)  ; skip first line
     (let* ((fields (string-split (read-line port) #\tab))
@@ -34,4 +59,6 @@ exec guile --debug -s "$0" "$@"
               (loop (read-line port)
                     (+ sum (truncate (* 1000 value))))))))))
 
-(test-end "external-gemma-run")
+(test-end "uvlmm-bimbam-gwa-run")
+
+!#