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# ===========================================================================
#
# PUBLIC DOMAIN NOTICE
# National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act. It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted. This software/database is freely available
# to the public for use. The National Library of Medicine and the U.S.
# Government have not placed any restriction on its use or reproduction.
#
# Although all reasonable efforts have been taken to ensure the accuracy
# and reliability of the software and data, the NLM and the U.S.
# Government do not and cannot warrant the performance or results that
# may be obtained by using this software or data. The NLM and the U.S.
# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
# purpose.
#
# Please cite the author in any work or product based on this material.
#
# ===========================================================================
# ===========================================================================
#
# This is the CMake build for sharq project.
#
# Usage
# cmake [options] <path-to-source>
#
# Parameter:
# path-to-source : path to this file's directory
#
# In addition, you can use all the standard CMake options, e.g.:
# -DCMAKE_BUILD_TYPE=<Debug|Release>
#
## ===========================================================================
if( SINGLE_CONFIG )
cmake_minimum_required(VERSION 3.16)
project(sharq)
## prefer static linkage
#set(CMAKE_FIND_LIBRARY_SUFFIXES .a .so .dylib .tbd)
find_package(ZLIB)
find_package(BZip2)
find_package (Threads)
# Debian ensures RE2 via Build-Depends
set( RE2_FOUND TRUE CACHE INTERNAL "" )
message(RE2_FOUND = ${RE2_FOUND} )
# RE2_FOUND will be used by sharQ tests
if ( ZLIB_FOUND AND BZip2_FOUND AND Threads_FOUND AND RE2_FOUND )
#set(CMAKE_VERBOSE_MAKEFILE ON)
set(CMAKE_CXX_STANDARD 17)
##specific to BitMagic
#if (COMPILER_OPTION_SSE42_SUPPORTED)
# add_definitions(-msse4.2 -DBMSSE42OPT)
#endif()
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_LIBRARY_OUTPUT_DIRECTORY})
set(LOCAL_BUILD_DIR ${CMAKE_ARCHIVE_OUTPUT_DIRECTORY})
set(LOCAL_INCDIR ${LOCAL_BUILD_DIR}/include)
set(LOCAL_LIBDIR ${LOCAL_BUILD_DIR}/lib)
# Google RE2 release
set(RE2_TAG 2021-09-01)
#set(RE2_TAG 2023-03-01)
# include (ExternalProject)
# ExternalProject_Add(RE2
# PREFIX ${LOCAL_BUILD_DIR}
# GIT_REPOSITORY ${RE2_URL}
# GIT_TAG ${RE2_TAG}
# BUILD_IN_SOURCE 1
# UPDATE_COMMAND "" # No update as we use specific tag
# INSTALL_DIR ${LOCAL_LIBDIR}
# INSTALL_COMMMAND ""
# CMAKE_ARGS
# -DCMAKE_BUILD_TYPE:STRING=Release
# -DRE2_BUILD_TESTING:BOOL=OFF
# -DCMAKE_INSTALL_PREFIX:PATH=${LOCAL_BUILD_DIR}
# -DCMAKE_INSTALL_LIBDIR:PATH=lib
# -DCMAKE_VERBOSE_MAKEFILE:BOOL=OFF
# -DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=ON
# -DCMAKE_INSTALL_MESSAGE:STRING=LAZY
# -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
# -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
# -DCMAKE_OSX_DEPLOYMENT_TARGET=${CMAKE_OSX_DEPLOYMENT_TARGET}
# )
set(RE2_STATIC_LIBRARIES -lre2 -labsl_string_view)
add_custom_target(
sharq.py
DEPENDS ${CMAKE_SOURCE_DIR}/tools/loaders/sharq/sharq.py
COMMAND ${CMAKE_COMMAND} -E copy
${CMAKE_SOURCE_DIR}/tools/loaders/sharq/sharq.py
${BINDIR}/sharq.py)
add_executable(sharq fastq_parse.cpp)
add_dependencies(sharq sharq.py)
target_include_directories(sharq PUBLIC ${LOCAL_INCDIR} ${CMAKE_SOURCE_DIR}/libs/inc ./ ../../../)
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
set(CXX_FILESYSTEM_LIBRARIES "stdc++fs")
endif()
target_link_libraries(sharq ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${COMMON_LIBS_READ})
MakeLinksExe( sharq false )
# if( RUN_SANITIZER_TESTS )
# set( asan_defs "-fsanitize=address" )
# add_executable(sharq-asan fastq_parse.cpp )
# add_dependencies(sharq-asan RE2 sharq.py)
# target_include_directories(sharq-asan PUBLIC ${LOCAL_INCDIR} ${CMAKE_SOURCE_DIR}/libs/inc ./ ../../../)
# target_link_libraries(sharq-asan ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
# target_compile_options( sharq-asan PRIVATE ${asan_defs} )
# target_link_options( sharq-asan PRIVATE ${asan_defs} )
#
# set( tsan_defs "-fsanitize=thread" )
# add_executable(sharq-tsan fastq_parse.cpp )
# add_dependencies(sharq-tsan RE2 sharq.py)
# target_include_directories(sharq-tsan PUBLIC ${LOCAL_INCDIR} ${CMAKE_SOURCE_DIR}/libs/inc ./ ../../../)
# target_link_libraries(sharq-tsan ${CXX_FILESYSTEM_LIBRARIES} ZLIB::ZLIB ${BZIP2_LIBRARIES} ${RE2_STATIC_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT})
# target_compile_options( sharq-tsan PRIVATE ${tsan_defs} )
# target_link_options( sharq-tsan PRIVATE ${tsan_defs} )
# endif()
else()
message( "SharQ is not built:" )
message( ZLIB_FOUND=${ZLIB_FOUND} )
message( BZip2_FOUND=${BZip2_FOUND} )
message( Threads_FOUND=${Threads_FOUND} )
message( RE2_FOUND=${RE2_FOUND} )
endif()
endif()
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