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CMakeLists.txt
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CMakeLists.txt
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# ----------------------------------------------------------------------------
# kSpider project
# ----------------------------------------------------------------------------
# Minimum cmake version
cmake_minimum_required (VERSION 3.14...3.20)
# Name of project and that it is C/C++.
project (
kSpider
LANGUAGES CXX C
VERSION 2.0.0
)
set(default_build_type "RELEASE")
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++17 -lstdc++fs -fPIC -lgomp -lrt -fopenmp -Ofast")
# ----------------------------------------------------------------------------
# kProcessor Setup
# ----------------------------------------------------------------------------
add_subdirectory(lib/kProcessor)
include_directories("${PROJECT_SOURCE_DIR}/lib/kProcessor/include/kProcessor")
include_directories("${PROJECT_SOURCE_DIR}/lib/kProcessor/ThirdParty/MQF/include")
set(kProcessor_INCLUDE_PATH "${PROJECT_SOURCE_DIR}/lib/kProcessor/include" "${PROJECT_SOURCE_DIR}/lib/kProcessor/include/kProcessor")
include_directories(${kProcessor_INCLUDE_PATH})
# ----------------------------------------------------------------------------
# END kProcessor Setup
# ----------------------------------------------------------------------------
include_directories("${PROJECT_SOURCE_DIR}/include")
include_directories("${PROJECT_SOURCE_DIR}/lib/argh")
include_directories("${PROJECT_SOURCE_DIR}/lib/json_parser/lib/include/")
add_subdirectory("lib/zstr")
set(PHMAP_INCLUDE_DIRS "${CMAKE_CURRENT_SOURCE_DIR}/lib/parallel-hashmap")
include_directories("${PHMAP_INCLUDE_DIRS}")
add_library(kSpider STATIC src/pairwise.cpp src/index.cpp src/fastx_to_kf.cpp src/sourmash_indexing.cpp src/bins_indexing.cpp ${PROJECT_SOURCE_DIR}/lib/kProcessor/include/kProcessor)
set_target_properties(kSpider PROPERTIES POSITION_INDEPENDENT_CODE 1 CXX_STANDARD 17)
target_link_libraries (kSpider kProcessor z)
target_link_libraries (kSpider kProcessor z zstr::zstr)
target_include_directories(kSpider INTERFACE ${PHMAP_INCLUDE_DIRS} ${PROJECT_SOURCE_DIR}/lib/kProcessor/include/kProcessor)
# add_executable(export_ccount export_colors_count.cpp)
# target_link_libraries(export_ccount kSpider kProcessor z)
add_executable(pairwise pairwise.cpp)
target_link_libraries(pairwise kSpider kProcessor z)
add_executable(index_bins bins.cpp)
target_link_libraries(index_bins kSpider kProcessor z)
add_executable(validate validate.cpp)
target_link_libraries(validate kSpider kProcessor z)
add_executable(dump_bin export_bin.cpp)
target_link_libraries(dump_bin kSpider kProcessor z)
add_executable(check_bin check_bin.cpp)
target_link_libraries(check_bin kSpider kProcessor z)
add_executable(dump_sig export_sig.cpp)
target_link_libraries(dump_sig kSpider kProcessor z)
add_executable(sigs_to_bins sigs_to_bins.cpp)
target_link_libraries(sigs_to_bins kSpider kProcessor z)
add_executable(sig_to_bin sig_to_bin.cpp)
target_link_libraries(sig_to_bin kSpider kProcessor z zstr::zstr)
add_executable(repr_sketches apps/repr_sketches.cpp)
target_link_libraries(repr_sketches z kProcessor)
# add_executable(index_kframes apps/index_kframes.cpp)
# target_link_libraries(index_kframes kSpider kProcessor z)
# add_executable(normalize apps/normalize_pe.cpp)
# target_link_libraries(normalize kSpider kProcessor z)
# add_executable(dump apps/dump_kframe.cpp)
# target_link_libraries(dump kSpider kProcessor z)
# add_executable(remove_percentile apps/remove_percentile.cpp)
# target_link_libraries(remove_percentile kSpider kProcessor z)
# add_executable(remove_singletones apps/remove_singletones.cpp)
# target_link_libraries(remove_singletones kSpider kProcessor z)
# add_executable(dump_count apps/dump_kmer_count.cpp)
# target_link_libraries(dump_count kSpider kProcessor z)
# add_executable(kmc_to_kfs apps/kmc_to_kfs.cpp)
# target_link_libraries(kmc_to_kfs kSpider kProcessor z)
# add_executable(percentile apps/percentile.cpp)
# target_link_libraries(percentile kSpider kProcessor z)