CMakeLists.txt

cmake_minimum_required(VERSION 2.6)

# project settings
project(mansagar)

##### General Compilation Settings
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --std=c++11  -Drestrict=__restrict__  -ffast-math -DpDNA=16 -DpPARSER=FASTP")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g -O0")
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG -march=native -funroll-loops")
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "${CMAKE_CXX_FLAGS_RELEASE} -g")
# Add these standard paths to the search paths for FIND_LIBRARY
# to find libraries from these locations first
if(UNIX)
  set(CMAKE_LIBRARY_PATH "${CMAKE_LIBRARY_PATH} /lib /usr/lib")
endif()

#Set default cmake build type
IF(NOT CMAKE_BUILD_TYPE)
  SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
    "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
    FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)


if(COMMAND cmake_policy)
  cmake_policy(SET CMP0003 NEW)
endif()

#### MPI
find_package(MPI REQUIRED)
if (MPI_FOUND)
  set(EXTRA_LIBS ${EXTRA_LIBS} ${MPI_LIBRARIES})
  include_directories(SYSTEM ${MPI_INCLUDE_PATH})
else (MPI_FOUND)
  message(SEND_ERROR "This application cannot compile without MPI")
endif (MPI_FOUND)

OPTION(ENABLE_BENCHMARKING "Enable benchmarking." ON)
# set here since timer needs to have this defined allways.
if (ENABLE_BENCHMARKING)
  SET(BL_BENCHMARK 1)
else(ENABLE_BENCHMARKING)
  SET(BL_BENCHMARK 0)
endif(ENABLE_BENCHMARKING)

###### Executable and Libraries
# Save libs and executables in the same place
set(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib CACHE PATH "Output directory for libraries" )
set(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH "Output directory for applications" )

# include external repositories : mxx, bliss
include_directories("${PROJECT_SOURCE_DIR}/ext")
#include_directories("${PROJECT_SOURCE_DIR}/ext/mxx/include")
#include_directories("${PROJECT_SOURCE_DIR}/ext/mxx/ext")

#BLISS
add_subdirectory("${PROJECT_SOURCE_DIR}/ext/bliss")   #BLISS cmake needs to be executed
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/src/")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/mxx/include")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/mxx/ext")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/tclap-1.2.1/include")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/Nadeau")
include_directories("${PROJECT_SOURCE_DIR}/ext/bliss/ext/sparsehash/src")

#include our build directory for bliss config files
include_directories("${CMAKE_BINARY_DIR}")


# include our src files
include_directories("${PROJECT_SOURCE_DIR}/src")
add_executable(find_seq_overlaps src/find_seq_overlaps.cpp src/io_utils.cpp)
target_link_libraries(find_seq_overlaps ${EXTRA_LIBS} bliss-utils)

add_executable(find_kmer_overlaps src/find_kmer_overlaps.cpp src/io_utils.cpp)
target_link_libraries(find_kmer_overlaps ${EXTRA_LIBS} bliss-utils)

add_executable(length_hist src/length_hist.cpp src/io_utils.cpp)
target_link_libraries(length_hist ${EXTRA_LIBS} bliss-utils)