-
Notifications
You must be signed in to change notification settings - Fork 4
/
CMakeLists.txt
229 lines (186 loc) · 7.73 KB
/
CMakeLists.txt
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
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
cmake_minimum_required(VERSION 3.10)
project(leviosam CXX C)
set(PROJECT_URL "https://github.com/alshai/leviosam")
set(PROJECT_DESCRIPTION "leviosam: lifting over alignments between genomes")
set(CMAKE_CXX_STANDARD 14)
find_library(HTS_LIB hts)
if(NOT HTS_LIB)
message(FATAL_ERROR "htslib library not found. Please specify -D CMAKE_LIBRARY_PATH and -D CMAKE_INCLUDE_PATH in the CMake command")
endif()
find_library(SDSL_LIB sdsl)
if(NOT SDSL_LIB)
message(FATAL_ERROR "libsdsl not found. Please specify -D CMAKE_LIBRARY_PATH and -D CMAKE_INCLUDE_PATH in the CMake command")
endif()
message(" type ${CMAKE_BUILD_TYPE}")
# From https://www.mattkeeter.com/blog/2018-01-06-versioning/
execute_process(COMMAND git log --pretty=format:'%h' -n 1
OUTPUT_VARIABLE GIT_REV
ERROR_QUIET)
if ("${CMAKE_BUILD_TYPE}" STREQUAL "release")
else()
# Check whether we got any revision (which isn't
# always the case, e.g. when someone downloaded a zip
# file from Github instead of a checkout)
if ("${GIT_REV}" STREQUAL "")
set(GIT_REV "")
set(GIT_DIFF "")
set(GIT_TAG "")
set(GIT_BRANCH "")
else()
execute_process(
COMMAND bash -c "git diff --quiet --exit-code || echo +"
OUTPUT_VARIABLE GIT_DIFF)
#execute_process(
# COMMAND git describe --exact-match --tags
# OUTPUT_VARIABLE GIT_TAG ERROR_QUIET)
execute_process(
COMMAND git rev-parse --abbrev-ref HEAD
OUTPUT_VARIABLE GIT_BRANCH)
string(STRIP "${GIT_REV}" GIT_REV)
string(SUBSTRING "${GIT_REV}" 1 7 GIT_REV)
string(STRIP "-${GIT_REV}" GIT_REV)
string(STRIP "${GIT_DIFF}" GIT_DIFF)
#string(STRIP "-${GIT_TAG}" GIT_TAG)
string(STRIP "-${GIT_BRANCH}" GIT_BRANCH)
endif()
set(VERSION
"#ifndef VERSION
#define VERSION \"5.2${GIT_BRANCH}${GIT_REV}${GIT_DIFF}\"
#endif
"
)
if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/src/version.hpp)
file(READ ${CMAKE_CURRENT_SOURCE_DIR}/src/version.hpp VERSION_)
else()
set(VERSION_ "")
endif()
if (NOT "${VERSION}" STREQUAL "${VERSION_}")
file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/src/version.hpp "${VERSION}")
endif()
endif()
include_directories(${CMAKE_INCLUDE_PATH})
# Check if SSE instructions are available on the machine where
# the project is compiled.
# From https://gist.github.com/hideo55/5642892
MACRO (FindSSE)
IF(CMAKE_SYSTEM_NAME MATCHES "Linux")
EXEC_PROGRAM(cat ARGS "/proc/cpuinfo" OUTPUT_VARIABLE CPUINFO)
STRING(FIND ${CPUINFO} "sse2" SSE2_TRUE)
IF (SSE2_TRUE)
set(SSE2_FOUND ON)
ELSE (SSE2_TRUE)
set(SSE2_FOUND OFF)
ENDIF (SSE2_TRUE)
STRING(FIND ${CPUINFO} "sse4_1" SSE4_1_TRUE)
IF (SSE4_1_TRUE)
set(SSE4_1_FOUND ON)
ELSE (SSE4_1_TRUE)
set(SSE4_1_FOUND OFF)
ENDIF (SSE4_1_TRUE)
ELSEIF(CMAKE_SYSTEM_NAME MATCHES "Darwin")
EXEC_PROGRAM("/usr/sbin/sysctl -n machdep.cpu.features" OUTPUT_VARIABLE
CPUINFO)
STRING(FIND ${CPUINFO} "SSE2" SSE2_TRUE)
IF (SSE2_TRUE)
set(SSE2_FOUND ON)
ELSE (SSE2_TRUE)
set(SSE2_FOUND OFF)
ENDIF (SSE2_TRUE)
STRING(FIND ${CPUINFO} "SSE4.1" SSE4_1_TRUE)
IF (SSE4_1_TRUE)
set(SSE4_1_FOUND ON)
ELSE (SSE4_1_TRUE)
set(SSE4_1_FOUND OFF)
ENDIF (SSE4_1_TRUE)
# ELSEIF(CMAKE_SYSTEM_NAME MATCHES "Windows")
# # TODO
# set(SSE2_FOUND true CACHE BOOL "SSE2 available on host")
# set(SSE3_FOUND false CACHE BOOL "SSE3 available on host")
# set(SSSE3_FOUND false CACHE BOOL "SSSE3 available on host")
# set(SSE4_1_FOUND false CACHE BOOL "SSE4.1 available on host")
# set(SSE4_2_FOUND false CACHE BOOL "SSE4.2 available on host")
# ELSE(CMAKE_SYSTEM_NAME MATCHES "Linux")
# set(SSE2_FOUND true CACHE BOOL "SSE2 available on host")
# set(SSE3_FOUND false CACHE BOOL "SSE3 available on host")
# set(SSSE3_FOUND false CACHE BOOL "SSSE3 available on host")
# set(SSE4_1_FOUND false CACHE BOOL "SSE4.1 available on host")
# set(SSE4_2_FOUND false CACHE BOOL "SSE4.2 available on host")
ENDIF(CMAKE_SYSTEM_NAME MATCHES "Linux")
# IF(CMAKE_COMPILER_IS_GNUCXX)
# EXECUTE_PROCESS(COMMAND ${CMAKE_CXX_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION)
# IF(GCC_VERSION VERSION_LESS 4.2)
# set(SSE4_1_FOUND false CACHE BOOL "SSE4.1 available on host" FORCE)
# set(SSE4_2_FOUND false CACHE BOOL "SSE4.2 available on host" FORCE)
# ENDIF()
# ENDIF(CMAKE_COMPILER_IS_GNUCXX)
if(SSE4_1_FOUND)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -msse4.1")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1")
# message("CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
elseif(SSE2_FOUND)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -msse2")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse2")
# message("CXX_FLAGS: ${CMAKE_CXX_FLAGS}")
endif(SSE4_1_FOUND)
mark_as_advanced(SSE2_FOUND SSE3_FOUND SSSE3_FOUND SSE4_1_FOUND SSE4_2_FOUND)
ENDMACRO(FindSSE)
FindSSE()
file(GLOB LIB_SOURCES src/reconcile.cpp src/lift_bed.cpp src/collate.cpp src/chain.cpp
src/leviosam_utils.cpp src/bed.cpp src/lift_bed.cpp src/aln.cpp
src/yaml.cpp
src/ksw2_extd2_sse.c src/ksw2_extz2_sse.c src/ksw2_extz.c
src/bam_md.c src/bam_aux.c src/gzstream.C)
file(GLOB LIB_HEADERS src/leviosam.hpp
src/reconcile.hpp src/lift_bed.hpp src/collate.hpp src/chain.hpp
src/leviosam_utils.hpp src/bed.hpp src/lift_bed.hpp src/aln.hpp
src/yaml.hpp src/rapidyaml.hpp
src/ksw.h
src/bam.h src/IITree.h src/gzstream.h)
add_library(lvsam ${LIB_SOURCES} ${LIB_HEADERS})
add_executable(leviosam src/leviosam.cpp)
target_link_libraries(leviosam lvsam)
target_link_libraries(leviosam ${HTS_LIB})
target_link_libraries(leviosam ${SDSL_LIB})
target_link_libraries(leviosam pthread)
target_link_libraries(leviosam z)
# Download and unpack googletest at configure time
configure_file(CMakeLists.txt.in googletest-download/CMakeLists.txt)
execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
RESULT_VARIABLE result
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download )
if(result)
message(FATAL_ERROR "CMake step for googletest failed: ${result}")
endif()
execute_process(COMMAND ${CMAKE_COMMAND} --build .
RESULT_VARIABLE result
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/googletest-download )
if(result)
message(FATAL_ERROR "Build step for googletest failed: ${result}")
endif()
# Prevent overriding the parent project's compiler/linker
# settings on Windows
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
enable_testing()
# Add googletest directly to our build. This defines
# the gtest and gtest_main targets.
add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/googletest-src
${CMAKE_CURRENT_BINARY_DIR}/googletest-build
EXCLUDE_FROM_ALL)
add_executable(leviosam_test src/leviosam_test.cpp)
target_link_libraries(leviosam_test lvsam)
target_link_libraries(leviosam_test ${HTS_LIB})
target_link_libraries(leviosam_test ${SDSL_LIB})
target_link_libraries(leviosam_test gtest gtest_main)
add_test(NAME leviosam_test COMMAND leviosam_test
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/testdata
)
add_executable(chain_test src/chain_test.cpp)
target_link_libraries(chain_test lvsam)
target_link_libraries(chain_test ${HTS_LIB})
target_link_libraries(chain_test ${SDSL_LIB})
target_link_libraries(chain_test gtest gtest_main)
add_test(NAME chain_test COMMAND chain_test
WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/testdata
)
INSTALL(TARGETS leviosam DESTINATION bin)
INSTALL(FILES src/leviosam.hpp DESTINATION include)