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|
#add_subdirectory(third_party)
if(MSVC)
# We need full support for C++ exceptions
add_compile_options(/EHsc)
# -Wall -Wextra -pedantic
add_compile_options(/W4)
# 'argument' : conversion from 'type1' to 'type2', possible loss of data
add_compile_options(/wd4244)
# 'type' : class 'type1' needs to have dll-interface to be used by clients of class 'type2'
# This is due to the fact that we're using STL containers in the interface
add_compile_options(/wd4251)
# 'var' : conversion from 'size_t' to 'type', possible loss of data
add_compile_options(/wd4267)
# cast truncates constant value
add_compile_options(/wd4310)
# declaration of 'identifier' hides previous local declaration
add_compile_options(/wd4456)
# 'strcat': This function or variable may be unsafe
add_compile_options(/wd4996)
else()
add_compile_options(-Wall -Wextra -pedantic)
# define compiler flags for all code, copied from Autoconf's AC_SYS_LARGEFILE
add_definitions(-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE)
endif()
###########
# library #
###########
# needed for reading compressed BAM files
find_package(ZLIB REQUIRED)
# create main BamTools API library
add_library(
BamTools
api/BamAlignment.cpp
api/BamMultiReader.cpp
api/BamReader.cpp
api/BamWriter.cpp
api/SamHeader.cpp
api/SamProgram.cpp
api/SamProgramChain.cpp
api/SamReadGroup.cpp
api/SamReadGroupDictionary.cpp
api/SamSequence.cpp
api/SamSequenceDictionary.cpp
api/internal/bam/BamHeader_p.cpp
api/internal/bam/BamMultiReader_p.cpp
api/internal/bam/BamRandomAccessController_p.cpp
api/internal/bam/BamReader_p.cpp
api/internal/bam/BamWriter_p.cpp
api/internal/index/BamIndexFactory_p.cpp
api/internal/index/BamStandardIndex_p.cpp
api/internal/index/BamToolsIndex_p.cpp
api/internal/io/BamDeviceFactory_p.cpp
api/internal/io/BamFile_p.cpp
api/internal/io/BamFtp_p.cpp
api/internal/io/BamHttp_p.cpp
api/internal/io/BamPipe_p.cpp
api/internal/io/BgzfStream_p.cpp
api/internal/io/ByteArray_p.cpp
api/internal/io/HostAddress_p.cpp
api/internal/io/HostInfo_p.cpp
api/internal/io/HttpHeader_p.cpp
api/internal/io/ILocalIODevice_p.cpp
api/internal/io/RollingBuffer_p.cpp
api/internal/io/TcpSocketEngine_p.cpp
api/internal/io/TcpSocket_p.cpp
api/internal/sam/SamFormatParser_p.cpp
api/internal/sam/SamFormatPrinter_p.cpp
api/internal/sam/SamHeaderValidator_p.cpp
api/internal/utils/BamException_p.cpp
)
# The SONAME is bumped on every version increment
# as Bamtools does not yet guarantee a stable ABI
set_target_properties(
BamTools PROPERTIES
SOVERSION ${BamTools_VERSION}
OUTPUT_NAME bamtools
CXX_STANDARD 11
CXX_STANDARD_REQUIRED ON
CXX_EXTENSIONS OFF)
target_include_directories(
BamTools PRIVATE
${ZLIB_INCLUDE_DIRS}
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR})
target_link_libraries(
BamTools PRIVATE
${ZLIB_LIBRARIES})
if(WIN32)
target_link_libraries(
BamTools PRIVATE
wsock32 ws2_32)
target_sources(
BamTools PRIVATE
api/internal/io/TcpSocketEngine_win_p.cpp)
else()
target_sources(
BamTools PRIVATE
api/internal/io/TcpSocketEngine_unix_p.cpp)
endif()
if(EnableNodeJS)
target_compile_definitions(
BamTools PRIVATE
SYSTEM_NODEJS=1)
endif()
# convenience library
add_library(
BamTools-utils
STATIC
utils/bamtools_fasta.cpp
utils/bamtools_options.cpp
utils/bamtools_pileup_engine.cpp
utils/bamtools_utilities.cpp
)
set_target_properties(
BamTools-utils PROPERTIES
CXX_STANDARD 11
CXX_STANDARD_REQUIRED ON
CXX_EXTENSIONS OFF)
target_include_directories(
BamTools-utils PRIVATE
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR})
target_link_libraries(
BamTools-utils PRIVATE
BamTools)
####################
# main application #
####################
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/toolkit/bamtools_version.h.in
${CMAKE_CURRENT_BINARY_DIR}/bamtools_version.h
@ONLY)
add_executable(
bamtools_cmd
toolkit/bamtools.cpp
toolkit/bamtools_convert.cpp
toolkit/bamtools_count.cpp
toolkit/bamtools_coverage.cpp
toolkit/bamtools_filter.cpp
toolkit/bamtools_header.cpp
toolkit/bamtools_index.cpp
toolkit/bamtools_merge.cpp
toolkit/bamtools_random.cpp
toolkit/bamtools_resolve.cpp
toolkit/bamtools_revert.cpp
toolkit/bamtools_sort.cpp
toolkit/bamtools_split.cpp
toolkit/bamtools_stats.cpp
${CMAKE_CURRENT_BINARY_DIR}/bamtools_version.h
)
set_target_properties(
bamtools_cmd PROPERTIES
OUTPUT_NAME bamtools
CXX_STANDARD 11
CXX_STANDARD_REQUIRED ON
CXX_EXTENSIONS OFF)
target_include_directories(
bamtools_cmd PRIVATE
${JSONCPP_INCLUDE_DIRS}
${CMAKE_CURRENT_SOURCE_DIR}
${CMAKE_CURRENT_BINARY_DIR})
target_link_libraries(
bamtools_cmd PRIVATE
BamTools BamTools-utils ${JSONCPP_LDFLAGS})
##############
# visibility #
##############
# can't inline this here, since we need to
# emulate the source tree and its includes.
add_subdirectory(api)
###################
# install targets #
###################
install(
TARGETS BamTools
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
install(
TARGETS bamtools_cmd
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
install(
FILES
api/BamAlgorithms.h
api/BamAlignment.h
api/BamAux.h
api/BamConstants.h
api/BamIndex.h
api/BamMultiReader.h
api/BamReader.h
api/BamWriter.h
api/IBamIODevice.h
api/SamConstants.h
api/SamHeader.h
api/SamProgram.h
api/SamProgramChain.h
api/SamReadGroup.h
api/SamReadGroupDictionary.h
api/SamSequence.h
api/SamSequenceDictionary.h
api/api_global.h
${CMAKE_CURRENT_BINARY_DIR}/api/bamtools_api_export.h
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bamtools/api
COMPONENT Development)
install(
FILES
api/algorithms/Sort.h
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bamtools/api/algorithms
COMPONENT Development)
install(
FILES
shared/bamtools_global.h
DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/bamtools/shared
COMPONENT Development)
# pkg-config
configure_file(
${CMAKE_CURRENT_SOURCE_DIR}/bamtools.pc.in
${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc
@ONLY)
install(
FILES
${CMAKE_CURRENT_BINARY_DIR}/bamtools-1.pc
DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig
COMPONENT Development)
|
