# 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})