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# Copyright (C) 2019 Intel Corporation. All rights reserved.
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
cmake_minimum_required (VERSION 3.14)
project(bwa_wasm C)
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
################ dependencies ################
find_package(Binaryen 111 REQUIRED)
################ LIBZ ################
set(LIBZ_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../libz)
add_library(z_wasm STATIC
${LIBZ_SRC_DIR}/adler32.c
${LIBZ_SRC_DIR}/compress.c
${LIBZ_SRC_DIR}/crc32.c
${LIBZ_SRC_DIR}/deflate.c
${LIBZ_SRC_DIR}/gzclose.c
${LIBZ_SRC_DIR}/gzlib.c
${LIBZ_SRC_DIR}/gzread.c
${LIBZ_SRC_DIR}/gzwrite.c
${LIBZ_SRC_DIR}/infback.c
${LIBZ_SRC_DIR}/inffast.c
${LIBZ_SRC_DIR}/inflate.c
${LIBZ_SRC_DIR}/inftrees.c
${LIBZ_SRC_DIR}/trees.c
${LIBZ_SRC_DIR}/uncompr.c
${LIBZ_SRC_DIR}/zutil.c
)
set_target_properties(z_wasm PROPERTIES LINKER_LANGUAGE C)
target_compile_definitions(z_wasm PRIVATE Z_HAVE_UNISTD_H _LARGEFILE64_SOURCE=1)
target_compile_options(z_wasm
PRIVATE
-Wno-unused-function
-Wno-unused-variable
)
target_include_directories(z_wasm
PUBLIC
${LIBZ_SRC_DIR}
)
################ BWA_WASM ################
set(BWA_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR})
set(BWA_SOURCE
${BWA_SRC_DIR}/utils.c
${BWA_SRC_DIR}/kthread.c
${BWA_SRC_DIR}/kstring.c
${BWA_SRC_DIR}/ksw.c
${BWA_SRC_DIR}/bwt.c
${BWA_SRC_DIR}/bntseq.c
${BWA_SRC_DIR}/bwa.c
${BWA_SRC_DIR}/bwamem.c
${BWA_SRC_DIR}/bwamem_pair.c
${BWA_SRC_DIR}/bwamem_extra.c
${BWA_SRC_DIR}/malloc_wrap.c
${BWA_SRC_DIR}/QSufSort.c
${BWA_SRC_DIR}/bwt_gen.c
${BWA_SRC_DIR}/rope.c
${BWA_SRC_DIR}/rle.c
${BWA_SRC_DIR}/is.c
${BWA_SRC_DIR}/bwtindex.c
${BWA_SRC_DIR}/bwashm.c
${BWA_SRC_DIR}/bwase.c
${BWA_SRC_DIR}/bwaseqio.c
${BWA_SRC_DIR}/bwtgap.c
${BWA_SRC_DIR}/bwtaln.c
${BWA_SRC_DIR}/bamlite.c
${BWA_SRC_DIR}/bwape.c
${BWA_SRC_DIR}/kopen.c
${BWA_SRC_DIR}/pemerge.c
${BWA_SRC_DIR}/maxk.c
${BWA_SRC_DIR}/bwtsw2_core.c
${BWA_SRC_DIR}/bwtsw2_main.c
${BWA_SRC_DIR}/bwtsw2_aux.c
${BWA_SRC_DIR}/bwt_lite.c
${BWA_SRC_DIR}/bwtsw2_chain.c
${BWA_SRC_DIR}/fastmap.c
${BWA_SRC_DIR}/bwtsw2_pair.c
${BWA_SRC_DIR}/main.c
)
add_executable(${PROJECT_NAME} ${BWA_SOURCE})
set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME bwa.wasm)
target_compile_definitions(${PROJECT_NAME}
PRIVATE
USE_MALLOC_WRAPPERS
__SSE__ __SSE2__ __SSE4_1__
_WASI_EMULATED_MMAN _WASI_EMULATED_SIGNAL _WASI_EMULATED_PROCESS_CLOCKS
)
target_compile_options(${PROJECT_NAME}
PRIVATE
-Wno-unused-function
-Wno-unused-variable
-msimd128
)
target_link_options(${PROJECT_NAME}
PRIVATE
-Wno-unused-command-line-argument
LINKER:--allow-undefined,--export=__heap_base,--export=__data_end
LINKER:-z,stack-size=1048576
)
target_link_libraries(${PROJECT_NAME} z_wasm wasi-emulated-process-clocks)
add_custom_target(bwa_wasm_opt ALL
COMMAND
${Binaryen_WASM_OPT} -Oz --enable-simd -o bwa.opt.wasm bwa.wasm
BYPRODUCTS
${CMAKE_CURRENT_BINARY_DIR}/bwa.opt.wasm
WORKING_DIRECTORY
${CMAKE_CURRENT_BINARY_DIR}
)
add_dependencies(bwa_wasm_opt ${PROJECT_NAME})
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