includ eunit test

Makefile.am

@@ -63,7 +63,8 @@ unit_tests_SOURCES = $(common_src) \
 					 tests/unittest/test_utilities.cpp \
 					 tests/unittest/test_panel.cpp \
 					 tests/unittest/test_mcmc.cpp \
-					 tests/unittest/test_updatePairHap.cpp
+					 tests/unittest/test_updatePairHap.cpp \
+					 tests/unittest/test_workflow.cpp
 
 unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
 unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)
@@ -79,7 +80,7 @@ io_unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)
 
 current_unit_tests_SOURCES = $(common_src) \
 					 tests/unittest/test_runner.cpp \
-					 tests/unittest/test_mcmc.cpp
+					 tests/unittest/test_workflow.cpp
 
 current_unit_tests_CXXFLAGS = $(common_flags) -DNDEBUG -DUNITTEST -Wno-write-strings --coverage
 current_unit_tests_LDADD    = -lcppunit -ldl $(common_LDADD)

tests/unittest/test_workflow.cpp

@@ -0,0 +1,56 @@
+/*
+ * dEploid is used for deconvoluting Plasmodium falciparum genome from
+ * mix-infected patient sample.
+ *
+ * Copyright (C) 2016-2018 University of Oxford
+ *
+ * Author: Sha (Joe) Zhu
+ *
+ * This file is part of dEploid.
+ *
+ * dEploid is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <cppunit/TestCase.h>
+#include <cppunit/extensions/HelperMacros.h>
+#include "src/dEploidIO.hpp"
+
+class TestWorkflow : public CppUnit::TestCase {
+    CPPUNIT_TEST_SUITE(TestWorkflow);
+    CPPUNIT_TEST(testWorkflowBest);
+    CPPUNIT_TEST_SUITE_END();
+
+ public:
+    void setUp() {
+    }
+
+    void tearDown() {
+    }
+
+    void testWorkflowBest(){
+        char *argv1[] = { "./dEploid",
+                         "-vcf", "data/testData/PG0390-C.test.vcf.gz",
+                         "-sample", "PG0390-C", "-plafFromVcf",
+                         "-exclude", "data/testData/labStrains.test.exclude.txt.gz"
+                         "-panel", "data/testData/labStrains.test.panel.txt.gz",
+                         "-best"};
+        DEploidIO tmp(11, argv1);
+        CPPUNIT_ASSERT_NO_THROW(tmp.workflow_best());
+
+    }
+};
+
+CPPUNIT_TEST_SUITE_REGISTRATION(TestWorkflow);
+