Merge pull request #5 from PROBIC/dev

mSWEEP-v1.4.0 (10 March 2020)

CMakeLists.txt

@@ -4,12 +4,34 @@ project(mSWEEP)
 ## Determine build type
 if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Release) ## Build Release by default
+elseif(CMAKE_BUILD_TYPE MATCHES Debug)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -g")
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -g")
+endif()
+
+if(CMAKE_BUILD_TYPE MATCHES Release)
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -xHost -fp-model fast=2 -no-prec-div -fimf-use-svml=true -ipo -m64")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -O3 -xHost -fp-model fast=2 -no-prec-div -fimf-use-svml=true -ipo -m64")
+    set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -O3 -xHost -fp-model fast=2 -no-prec-div -fimf-use-svml=true -ipo -m64")
+  else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -ffast-math -funroll-loops")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -ffast-math -funroll-loops")
+    set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -ffast-math -funroll-loops")
+  endif()
 endif()
 
 ## Check dependencies
-find_package(Threads REQUIRED)
-set(THREADS_PREFER_PTHREAD_FLAG ON)
-find_package(ZLIB)
+find_package(OpenMP)
+if (OPENMP_FOUND)
+  set(MSWEEP_OPENMP_SUPPORT 1)
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_GLIBCXX_PARALLEL")
+  set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -D_GLIBCXX_PARALLEL")
+  set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -D_GLIBCXX_PARALLEL")
+else()
+  set(MSWEEP_OPENMP_SUPPORT 0)
+endif()
 set (CMAKE_CXX_STANDARD 11)
 set (CMAKE_CXX_STANDARD_REQUIRED ON)
 
@@ -35,6 +57,36 @@ string(TIMESTAMP _BUILD_TIMESTAMP)
 
 ## Generate a version.h file containing build version and timestamp
 configure_file(include/version.h.in ${CMAKE_BINARY_DIR}/include/version.h @ONLY)
+configure_file(include/openmp_config.hpp.in ${CMAKE_BINARY_DIR}/include/openmp_config.hpp @ONLY)
+
+add_executable(mSWEEP
+${CMAKE_SOURCE_DIR}/src/BootstrapSample.cpp
+${CMAKE_SOURCE_DIR}/src/Reference.cpp
+${CMAKE_SOURCE_DIR}/src/Sample.cpp
+${CMAKE_SOURCE_DIR}/src/likelihood.cpp
+${CMAKE_SOURCE_DIR}/src/main.cpp
+${CMAKE_SOURCE_DIR}/src/matrix.cpp
+${CMAKE_SOURCE_DIR}/src/parse_arguments.cpp
+${CMAKE_SOURCE_DIR}/src/process_reads.cpp
+${CMAKE_SOURCE_DIR}/src/rcg.cpp
+${CMAKE_SOURCE_DIR}/src/read_bitfield.cpp)
+
+## Check supported compression types
+find_package(BZip2)
+if (BZIP2_FOUND)
+  include_directories(${BZIP2_INCLUDE_DIRS})
+  target_link_libraries(mSWEEP ${BZIP2_LIBRARIES})
+endif()    
+find_package(LibLZMA)
+if (LIBLZMA_FOUND)
+  include_directories(${LIBLZMA_INCLUDE_DIRS})
+  target_link_libraries(mSWEEP ${LIBLZMA_LIBRARIES})
+endif()
+find_package(ZLIB)
+if (ZLIB_FOUND)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  target_link_libraries(mSWEEP ${ZLIB_LIBRARIES})
+endif()
 
 if(NOT ZLIB_FOUND OR CMAKE_BUILD_ZLIB)
   configure_file(CMakeLists.txt.in ${CMAKE_BINARY_DIR}/external/zlib-download/CMakeLists.txt)
@@ -55,15 +107,60 @@ else()
   set(ZLIB ZLIB::ZLIB)
 endif()
 
-add_subdirectory(${CMAKE_SOURCE_DIR}/external/telescope
-                 ${CMAKE_BINARY_DIR}/external/telescope/build)
-set_target_properties(telescope PROPERTIES EXCLUDE_FROM_ALL 1)
+## Check dependencies and download them if not given
+## telescope
+if (DEFINED CMAKE_TELESCOPE_LIBRARY AND DEFINED CMAKE_TELESCOPE_HEADERS)
+  find_library(TELESCOPE NAMES telescope HINTS ${CMAKE_TELESCOPE_LIBRARY})
+  target_link_libraries(mSWEEP ${TELESCOPE})
+  include_directories("${CMAKE_TELESCOPE_HEADERS}")
+else()
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-telescope.txt.in ${CMAKE_BINARY_DIR}/external/telescope-download/CMakeLists.txt)
+  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
+    RESULT_VARIABLE result
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/telescope-download )
+  if(result)
+    message(FATAL_ERROR "CMake step for telescope failed: ${result}")
+  endif()
+  execute_process(COMMAND ${CMAKE_COMMAND} --build .
+    RESULT_VARIABLE result
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/telescope-download )
+  if(result)
+    message(FATAL_ERROR "Build step for telescope failed: ${result}")
+  endif()
+  add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/external/telescope
+                   ${CMAKE_CURRENT_BINARY_DIR}/external/telescope/build)
+  include_directories(${CMAKE_CURRENT_BINARY_DIR}/external/telescope/include)
+  set_target_properties(telescope PROPERTIES EXCLUDE_FROM_ALL 1)
+  target_link_libraries(mSWEEP libtelescope)
+endif()
 
-include_directories(${CMAKE_SOURCE_DIR}/include ${CMAKE_BINARY_DIR}/include ${CMAKE_SOURCE_DIR}/external/zstr ${CMAKE_SOURCE_DIR}/external ${CMAKE_SOURCE_DIR}/include/tools)
-file(GLOB SOURCES "src/*.cpp")
+## bxzstr
+if (DEFINED CMAKE_BXZSTR_LIBRARY AND DEFINED CMAKE_BXZSTR_HEADERS)
+  find_library(BXZSTR NAMES telescope HINTS ${CMAKE_BXZSTR_LIBRARY})
+  include_directories("${CMAKE_BXZSTR_HEADERS}")
+else()
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/config/CMakeLists-bxzstr.txt.in ${CMAKE_BINARY_DIR}/external/bxzstr-download/CMakeLists.txt)
+  execute_process(COMMAND ${CMAKE_COMMAND} -G "${CMAKE_GENERATOR}" .
+    RESULT_VARIABLE result
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/bxzstr-download )
+  if(result)
+    message(FATAL_ERROR "CMake step for bxzstr failed: ${result}")
+  endif()
+  execute_process(COMMAND ${CMAKE_COMMAND} --build .
+    RESULT_VARIABLE result
+    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/external/bxzstr-download )
+  if(result)
+    message(FATAL_ERROR "Build step for bxzstr failed: ${result}")
+  endif()
+  add_subdirectory(${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr
+                   ${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr/build)
+  include_directories(${CMAKE_CURRENT_BINARY_DIR}/external/bxzstr/include)
+endif()
 
-add_executable(mSWEEP ${SOURCES})
-add_executable(matchfasta ${CMAKE_SOURCE_DIR}/src/tools/matchfasta.cpp)
+include_directories(${CMAKE_SOURCE_DIR}/include
+${CMAKE_SOURCE_DIR}/external ${CMAKE_SOURCE_DIR}/include/tools
+${CMAKE_SOURCE_DIR}/external/cxxio
+${CMAKE_CURRENT_BINARY_DIR}/include)
 
 ## Handle compiling zlib from source
 if(CMAKE_BUILD_ZLIB)
@@ -75,5 +172,14 @@ if(CMAKE_BUILD_ZLIB)
   add_dependencies(mSWEEP zlibstatic)
 endif()
 
+add_library(msweeptools ${CMAKE_CURRENT_SOURCE_DIR}/src/tools/matchfasta.cpp)
+add_executable(matchfasta ${CMAKE_CURRENT_SOURCE_DIR}/src/tools/main.cpp)
+
 # Link libraries
-target_link_libraries(mSWEEP Threads::Threads ${ZLIB} libtelescope)
+target_link_libraries(mSWEEP ${ZLIB} msweeptools)
+target_link_libraries(matchfasta msweeptools)
+if (OPENMP_FOUND)
+  target_link_libraries(mSWEEP OpenMP::OpenMP_CXX)
+  target_link_libraries(matchfasta OpenMP::OpenMP_CXX)
+  target_link_libraries(msweeptools OpenMP::OpenMP_CXX)
+endif()