1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
|
cmake_minimum_required(VERSION 3.2)
project(minimac4 VERSION 4.1.2)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose build type (Debug|Release|RelWithDebInfo|MinSizeRel)" FORCE)
endif()
set(CMAKE_CXX_STANDARD 11)
add_definitions(-DVERSION="${PROJECT_VERSION}")
#set(CMAKE_FIND_LIBRARY_SUFFIXES ".a;${CMAKE_FIND_LIBRARY_SUFFIXES}") # Prefer libz.a when both are available
#find_package(OpenMP)
#if (OPENMP_FOUND)
# set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
# set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
#endif()
find_package(Threads)
find_library(OMPP_LIBRARY omp)
find_package(savvy REQUIRED)
add_executable(minimac4
src/dosage_writer.cpp src/dosage_writer.hpp
src/hidden_markov_model.cpp src/hidden_markov_model.hpp
src/input_prep.cpp src/input_prep.hpp
src/recombination.cpp src/recombination.hpp
src/unique_haplotype.cpp src/unique_haplotype.hpp
src/main.cpp)
target_link_libraries(minimac4 savvy ${OMPP_LIBRARY} lzma Threads::Threads)
if(BUILD_TESTS)
enable_testing()
add_test(simple_test ${CMAKE_SOURCE_DIR}/test/simple-test.sh ${CMAKE_BINARY_DIR}/minimac4 m4_simple_test_output ${CMAKE_SOURCE_DIR}/test/input/ref_panel.vcf ${CMAKE_SOURCE_DIR}/test/input/tar_panel.vcf)
add_test(haploid_and_diploid_test ${CMAKE_SOURCE_DIR}/test/simple-test.sh ${CMAKE_BINARY_DIR}/minimac4 m4_haploid_and_diploid_test_output ${CMAKE_SOURCE_DIR}/test/input/ref_panel_with_haploid_sample.vcf ${CMAKE_SOURCE_DIR}/test/input/tar_panel_with_haploid_sample.vcf)
endif()
install(TARGETS minimac4 RUNTIME DESTINATION bin)
set(CPACK_PACKAGE_VERSION_MAJOR ${PROJECT_VERSION_MAJOR})
set(CPACK_PACKAGE_VERSION_MINOR ${PROJECT_VERSION_MINOR})
set(CPACK_PACKAGE_VERSION_PATCH ${PROJECT_VERSION_PATCH})
include(CPack)
|
