diff --git a/.travis.yml b/.travis.yml
index c69a707..740c1e4 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,5 +11,6 @@ before_install:
 script:
   - ./functional_tests/biodemo-test.sh -p biodemo -d functional_tests/test_data
   - ./.travis/unit-test.sh
+  - coverage combine .coverage functional_tests/test_data/.coverage
   - codecov
 
diff --git a/functional_tests/biodemo-test.sh b/functional_tests/biodemo-test.sh
index 9b3cc9c..585c8d7 100755
--- a/functional_tests/biodemo-test.sh
+++ b/functional_tests/biodemo-test.sh
@@ -91,7 +91,7 @@ function parse_args {
 # ARG3: expected exit status
 function test_stdout_exit {
     let num_tests+=1
-    output=$(eval $1)
+    output=$(eval "coverage run -a ${1/$test_program/$(which $test_program)}")
     exit_status=$?
     expected_output_file=$2
     expected_exit_status=$3
@@ -125,7 +125,7 @@ function test_stdout_exit {
 # important
 function test_exit_status {
     let num_tests+=1
-    output=$(eval $1)
+    output=$(eval "coverage run -a ${1/$test_program/$(which $test_program)}")
     exit_status=$?
     expected_exit_status=$2
     verbose_message "Testing exit status: $1"