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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 2.8.12)
set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -O2")
enable_testing()
find_package (GTest REQUIRED)
find_package (Threads REQUIRED)
find_package (Protobuf REQUIRED)
include_directories(${GTEST_INCLUDE_DIRS})
find_package (Protobuf REQUIRED)
PROTOBUF_GENERATE_CPP(PROTO_SRCS PROTO_HDRS config.proto)
add_library(node node.cc)
add_executable(node_test node_test.cc)
target_link_libraries(node_test node ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
add_test(NodeTest node_test)
add_library(graph graph.cc)
target_link_libraries(graph node)
add_executable(graph_test graph_test.cc)
target_link_libraries(graph_test graph ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
add_test(GraphTest graph_test)
add_library(path path.cc)
target_link_libraries(path node)
add_executable(path_test path_test.cc)
target_link_libraries(path_test path ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} graph)
add_test(PathTest path_test)
add_library(dalign DALIGN/DB.c DALIGN/QV.c DALIGN/align.c)
add_library(dalign_wrapper Sequence.cc DalignWrapper.cc)
target_link_libraries(dalign_wrapper dalign)
add_library(read_set read_set.cc)
target_link_libraries(read_set dalign_wrapper)
add_executable(read_set_test read_set_test.cc)
target_link_libraries(read_set_test read_set ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
add_test(ReadSetTest read_set_test)
add_executable(util_test util_test.cc)
target_link_libraries(util_test ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
add_test(UtilTest util_test)
add_library(path_aligner path_aligner.cc)
target_link_libraries(path_aligner path read_set graph)
add_library(moves moves.cc)
target_link_libraries(moves path)
add_executable(moves_test moves_test.cc)
target_link_libraries(moves_test ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} moves)
add_test(MovesTest moves_test)
add_library(read_probability_calculator read_probability_calculator.cc ${PROTO_SRCS} ${PROTO_HDRS})
target_include_directories(read_probability_calculator PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
target_link_libraries(read_probability_calculator path_aligner ${PROTOBUF_LIBRARIES})
add_executable(read_probability_calculator_test read_probability_calculator_test.cc)
target_link_libraries(read_probability_calculator_test read_probability_calculator ${GTEST_BOTH_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
add_test(ReadProbabilityCalculatorTest read_probability_calculator_test)
add_executable(get_subgraph get_subgraph.cc)
target_link_libraries(get_subgraph graph)
add_executable(gaml gaml_main.cc ${PROTO_SRCS} ${PROTO_HDRS})
target_include_directories(gaml PUBLIC ${CMAKE_CURRENT_BINARY_DIR})
target_link_libraries(gaml graph path read_probability_calculator moves ${PROTOBUF_LIBRARIES})