CMakeLists.txt

cmake_minimum_required(VERSION 3.16.0)

project(fastF VERSION 1.0)

set(CMAKE_C_STANDARD 99)
set(CMAKE_BUILD_TYPE Debug)
set(CMAKE_C_COMPILER /home/yu89975/local/bin/gcc)
set(CMAKE_CXX_COMPILER /home/yu89975/local/bin/g++)
# set(CMAKE_BUILD_TYPE Release)

find_package(OpenMP REQUIRED)

include_directories(${CMAKE_SOURCE_DIR}/external/htslib/include)
link_directories(${CMAKE_SOURCE_DIR}/external/htslib/lib)
include_directories(${CMAKE_SOURCE_DIR}/external/criterion/include)
link_directories(${CMAKE_SOURCE_DIR}/external/criterion/lib)
include_directories(${CMAKE_SOURCE_DIR}/external/argparse/)
include_directories(${CMAKE_SOURCE_DIR}/external/mt19937ar.sep)
include_directories(${CMAKE_SOURCE_DIR}/external/hashtable)

set(SOURCES
    ./src/main.c
    external/argparse/argparse.c
    external/mt19937ar.sep/mt19937ar.c
    external/hashtable/hashtable.c
    ./src/filter.c
    ./src/count.c
    ./src/extract.c
    ./src/bam2db_ds.c
    ./src/utils.c
)

add_executable(fastF ${SOURCES})

target_link_libraries(fastF z pthread hts sqlite3)

# add_subdirectory(./test)