Add CMake support for building bowtie2 with libsais

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.1 FATAL_ERROR)
 
 cmake_policy(SET CMP0048 NEW)
 cmake_policy(SET CMP0005 NEW)
@@ -25,6 +25,7 @@ if (NOT CMAKE_BUILD_TYPE OR CMAKE_BUILD_TYPE STREQUAL "")
    set(CMAKE_BUILD_TYPE "Release" CACHE STRING "" FORCE)
 endif()
 set(USE_SRA ${USE_SRA})
+set(USE_SAIS ${USE_SAIS})
 set(WITH_THREAD_PROFILING ${WITH_THREAD_PROFILING})
 set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
@@ -152,17 +153,47 @@ elseif (${ARCH} MATCHES amd64|x64_64)
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse2")
 endif()
 
+if (WITH_THREAD_PROFILING)
+  add_definitions(-DPER_THREAD_TIMING=1)
+endif()
+
+if (CMAKE_BUILD_TYPE STREQUAL "Release")
+  add_definitions(-DNDEBUG)
+else()
+  message("--------------------------------------------------------------------------")
+  message("ATTN: Targets built in debug mode will have `-debug' appended to its name.")
+  message("See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html")
+  message("--------------------------------------------------------------------------")
+  set(CMAKE_EXECUTABLE_SUFFIX "-debug")
+endif()
+
+find_package(ZLIB REQUIRED)
+
+find_package(Threads REQUIRED)
+link_libraries(Threads::Threads)
+
+if (ZLIB_FOUND)
+  link_libraries(${ZLIB_LIBRARIES})
+  include_directories(${ZLIB_INCLUDE_DIRS})
+endif()
+
+include_directories(${PROJECT_SOURCE_DIR})
+get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)
+string(REPLACE ";" " -D" COMPILER_DEFS "${COMPILER_DEFS}")
+string(REPLACE "\"" "" COMPILER_DEFS "${COMPILER_DEFS}")
+add_definitions(-DCOMPILER_OPTIONS="${CMAKE_CXX_FLAGS} -D${COMPILER_DEFS}")
+
 if (USE_SRA)
   set(SRA_TOOLS_VER 3.0.9)
   set(NCBI_VDB_VER 3.0.9)
 
+  set(THIRD_PARTY_LIBS "${PROJECT_SOURCE_DIR}/third_party")
+
   find_package(Java COMPONENTS Development REQUIRED)
   find_package(PythonInterp REQUIRED)
   find_package(Perl REQUIRED)
   find_program(MAKE_EXE NAMES gmake nmake make)
 
-  set(THIRD_PARTY_LIBS "${PROJECT_SOURCE_DIR}/third_party")
-
   ExternalProject_add(ncbi_vdb_project
     URL https://github.com/ncbi/ncbi-vdb/archive/${NCBI_VDB_VER}.tar.gz
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/ncbi-vdb-${NCBI_VDB_VER}
@@ -172,12 +203,6 @@ if (USE_SRA)
     INSTALL_COMMAND ${MAKE_EXE} install
     )
 
-  # ExternalProject_Get_Property(ncbi_vdb_project SOURCE_DIR)
-  # set(NCBI_VDB_INSTALL_DIR ${SOURCE_DIR}/install)
-
-  # link_directories(${NCBI_VDB_INSTALL_DIR}/lib64)
-  # include_directories(${NCBI_VDB_INSTALL_DIR}/include)
-
   ExternalProject_add(ngs_project
     URL https://github.com/ncbi/sra-tools/archive/${SRA_TOOLS_VER}.tar.gz
     PREFIX ${CMAKE_CURRENT_BINARY_DIR}/sra-tools-${SRA_TOOLS_VER}
@@ -188,9 +213,6 @@ if (USE_SRA)
     DEPENDS ncbi_vdb_project
     )
 
-  # ExternalProject_Get_Property(ngs_project SOURCE_DIR)
-  # set(NGS_INSTALL_DIR ${SOURCE_DIR}/install)
-
   link_directories(${THIRD_PARTY_LIBS}/lib64)
   include_directories(${THIRD_PARTY_LIBS}/include)
 
@@ -204,39 +226,51 @@ if (USE_SRA)
   find_library(LIBNCBI_NGS ncbi-ngs-static PATHS ${THIRD_PARTY_LIBS}/lib64 NO_DEFAULT_PATH)
   set_property(TARGET ncbi-ngs-static PROPERTY IMPORTED_LOCATION ${LIBNCBI_NGS})
 
-  link_libraries(ncbi-ngs-static ncbi-vdb-static)
+  link_libraries(ncbi-ngs-static ncbi-vdb-static dl)
   add_definitions(-DUSE_SRA)
 endif()
 
-if (WITH_THREAD_PROFILING)
-  add_definitions(-DPER_THREAD_TIMING=1)
-endif()
+if (USE_SAIS)
+  set(LIBSAIS_VER 2.7.3)
+
+  find_package(OpenMP)
+  if (OpenMP_CXX_FOUND)
+    link_libraries(OpenMP::OpenMP_CXX)
+    ExternalProject_add(libsais_project
+      URL https://github.com/IlyaGrebnov/libsais/archive/refs/tags/v${LIBSAIS_VER}.tar.gz
+      PREFIX ${CMAKE_CURRENT_BINARY_DIR}/libsais-${LIBSAIS_VER}
+      BUILD_IN_SOURCE 1
+      DOWNLOAD_EXTRACT_TIMESTAMP false
+      CONFIGURE_COMMAND cmake . -D LIBSAIS_USE_OPENMP=1
+      BUILD_COMMAND cmake --build .
+      INSTALL_COMMAND ""
+    )
+  else()
+    ExternalProject_add(libsais_project
+      URL https://github.com/IlyaGrebnov/libsais/archive/refs/tags/v${LIBSAIS_VER}.tar.gz
+      PREFIX ${CMAKE_CURRENT_BINARY_DIR}/libsais-${LIBSAIS_VER}
+      BUILD_IN_SOURCE 1
+      DOWNLOAD_EXTRACT_TIMESTAMP false
+      CONFIGURE_COMMAND cmake .
+      BUILD_COMMAND cmake --build .
+      INSTALL_COMMAND ""
+    )
+  endif()
 
-if (CMAKE_BUILD_TYPE STREQUAL "Release")
-  add_definitions(-DNDEBUG)
-else()
-  message("--------------------------------------------------------------------------")
-  message("ATTN: Targets built in debug mode will have `-debug' appended to its name.")
-  message("See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html")
-  message("--------------------------------------------------------------------------")
-  set(CMAKE_EXECUTABLE_SUFFIX "-debug")
-endif()
 
-find_package(ZLIB REQUIRED)
+  add_library(libsais STATIC IMPORTED)
+  add_dependencies(libsais libsais_project)
 
-find_package(Threads REQUIRED)
-link_libraries(Threads::Threads)
+  ExternalProject_Get_Property(libsais_project SOURCE_DIR)
+  link_directories(${SOURCE_DIR})
+  include_directories(${SOURCE_DIR}/include)
 
-if (ZLIB_FOUND)
-  link_libraries(${ZLIB_LIBRARIES})
-  include_directories(${ZLIB_INCLUDE_DIRS})
-endif()
+  # find_library(LIBLIBSAIS libsais PATHS ${SOURCE_DIR} NO_DEFAULT_PATH)
+  set_property(TARGET libsais PROPERTY IMPORTED_LOCATION ${SOURCE_DIR}/liblibsais.a)
 
-include_directories(${PROJECT_SOURCE_DIR})
-get_directory_property(COMPILER_DEFS COMPILE_DEFINITIONS)
-string(REPLACE ";" " -D" COMPILER_DEFS "${COMPILER_DEFS}")
-string(REPLACE "\"" "" COMPILER_DEFS "${COMPILER_DEFS}")
-add_definitions(-DCOMPILER_OPTIONS="${CMAKE_CXX_FLAGS} -D${COMPILER_DEFS}")
+  link_libraries(libsais)
+  add_definitions(-DUSE_SAIS -DLIBSAIS_OPENMP)
+endif()
 
 add_executable(bowtie2-align-s ${SEARCH_CPPS} ${SHARED_CPPS})
 add_executable(bowtie2-align-l ${SEARCH_CPPS} ${SHARED_CPPS})