Feature test peeling

test/CMakeLists.txt

@@ -25,10 +25,13 @@ SET_TESTS_PROPERTIES(build_gitkeep PROPERTIES
   PASS_REGULAR_EXPRESSION "d41d8cd98f00b204e9800998ecf8427e"
 )
 
+
+
 ################################################################################
 # Compile unit tests
 include_directories(../src/include)
 
+
 # Make a test for each unit test file located in test/ dir
 file(GLOB_RECURSE TESTS test_*[cc|cpp])
 foreach(test ${TESTS})
@@ -49,6 +52,40 @@ foreach(test ${TESTS})
 endforeach(test)
 
 ################################################################################
+
+
+
+################################################################################
+# temp Compile unit tests with *.cc
+# TODO: Use a different filename pattern for now (test2_* instead of test_*).
+# TODO: How to add min *.cc files instead of all *.cc later?
+include_directories(./)
+
+file(GLOB_RECURSE TESTS2 "test2_*[cc|cpp]")
+foreach(test ${TESTS2})
+  get_filename_component(testName ${test} NAME_WE)
+  add_executable(${testName} EXCLUDE_FROM_ALL ${test}
+          ${CMAKE_SOURCE_DIR}/src/lib/peeling.cc
+          ##            ../src/lib/likelihood.cc ../src/lib/newick.cc ../src/lib/pedigree.cc
+          ##            ../src/lib/mutation.cc ../src/lib/stats.cc
+          )
+  target_link_libraries(${testName}
+          Threads::Threads
+          Boost::PROGRAM_OPTIONS
+          Boost::FILESYSTEM
+          Boost::SYSTEM
+          Boost::UNIT_TEST_FRAMEWORK
+          EIGEN3::EIGEN3
+          HTSLIB::HTSLIB
+          )
+  add_test(${testName}_build "${CMAKE_COMMAND}" --build ${CMAKE_BINARY_DIR} --target ${testName})
+  add_test(${testName}_run ${testName})
+  set_tests_properties(${testName}_run PROPERTIES DEPENDS ${testName}_build)
+endforeach(test)
+
+################################################################################
+
+
 # Full executable tests
 
 # Check if using download source package or running latest code inside a git repository

test/boost_test_helper.h

@@ -0,0 +1,65 @@
+//
+// Created by steven on 1/15/16.
+//
+// Replace some with with BOOST later
+//
+
+#ifndef DENOVOGEAR_BOOST_TEST_HELPER_H
+#define DENOVOGEAR_BOOST_TEST_HELPER_H
+
+#include <boost/test/test_tools.hpp>
+#include <boost/test/unit_test.hpp>
+
+//TODO: Where should this file go?
+//FIXME: too many global
+const double ABS_TEST_THRESHOLD = 1e-10;
+const double BOOST_CLOSE_THRESHOLD = 1e-6;
+
+template<typename A>
+void boost_check_array(A &expected, A &result, int expected_size) {
+
+    BOOST_CHECK_EQUAL(expected_size, expected.size());
+    BOOST_CHECK_EQUAL(expected.size(), result.size());
+    for (int i = 0; i < expected.size(); ++i) {
+        BOOST_CHECK_CLOSE(expected[i], result[i], BOOST_CLOSE_THRESHOLD);
+    }
+
+}
+
+template<typename M>
+void boost_check_matrix(M &expected, M &result, int expected_rows, int expected_cols) {
+    BOOST_CHECK_EQUAL(expected_rows, expected.rows());
+    BOOST_CHECK_EQUAL(expected_cols, expected.cols());
+    BOOST_CHECK_EQUAL(expected.rows(), result.rows());
+    BOOST_CHECK_EQUAL(expected.cols(), result.cols());
+
+    for (int i = 0; i < expected.rows(); ++i) {
+        for (int j = 0; j < expected.cols(); ++j) {
+            BOOST_CHECK_CLOSE(expected(i, j), result(i, j), BOOST_CLOSE_THRESHOLD);
+        }
+    }
+}
+
+
+template<typename A, typename B>
+void AssertTrue(A expected, B actual){
+    assert(expected==actual);
+};
+
+template<typename A>
+void AssertNear(A expected, A actual){
+    assert(((expected - actual)/expected) < ABS_TEST_THRESHOLD);
+
+};
+
+template<typename A>
+void AssertEigenMatrixNear(A expected, A actual){
+    for (int j = 0; j < expected.rows(); ++j) {
+        for (int k = 0; k < expected.cols(); ++k) {
+            AssertNear(expected(j,k), actual(j,k));
+        }
+    }
+};
+
+
+#endif //DENOVOGEAR_BOOST_TEST_HELPER_H