Commit e78087f6 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 0.18.0+dfsg

parent 143103ae

cmake/FindHTSlib.cmake

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# Find HTSlib

find_package(PkgConfig REQUIRED)

pkg_check_modules(HTSlib REQUIRED htslib)



# because CMake is trying to be extra clever,

# it will not properly load libraries with

# absolute paths in *_LIBRARIES

set(HTSlib_LIBRARIES "${HTSlib_LDFLAGS}")



message(STATUS "   HTSlib include dirs: ${HTSlib_INCLUDE_DIRS}")

message(STATUS "   HTSlib libraries: ${HTSlib_LIBRARIES}")

cmake/PbbamTool.cmake

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include(CMakeParseArguments)



function(create_pbbam_tool)



    # parse args

    set(oneValueArgs TARGET)

    set(multiValueArgs SOURCES)

    cmake_parse_arguments(create_pbbam_tool "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})



    # create executable

    include_directories(

        ${ToolsCommonDir}           # shared tool code

        ${GeneratedDir}             # generated version headers

        ${PacBioBAM_INCLUDE_DIRS}   # pbbam/htslib includes

    )

    add_executable(${create_pbbam_tool_TARGET} ${create_pbbam_tool_SOURCES})

    set_target_properties(

        ${create_pbbam_tool_TARGET} PROPERTIES

        RUNTIME_OUTPUT_DIRECTORY ${PacBioBAM_BinDir}

    )

    target_link_libraries(${create_pbbam_tool_TARGET} pbbam)



endfunction(create_pbbam_tool)

cmake/pbbam-ccache.cmake

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if(PacBioBAM_use_ccache)

    find_program(CCACHE_FOUND ccache)

    if(CCACHE_FOUND)

        set_property(GLOBAL PROPERTY RULE_LAUNCH_COMPILE ccache)

        set_property(GLOBAL PROPERTY RULE_LAUNCH_LINK    ccache)

    endif()

endif()

cmake/pbbam-compilerflags.cmake

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include(CheckCXXCompilerFlag)



# C++11 check & enabling

if (CMAKE_VERSION VERSION_LESS "3.1")

    if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")

        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")    # clang

    else()

        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")        # gcc

    endif()

else() # 3.1+

    set(CMAKE_CXX_STANDARD          14)

    set(CMAKE_CXX_STANDARD_REQUIRED ON)

endif()



# shared CXX flags for src & tests

if (MSVC)

    set(PacBioBAM_CXX_FLAGS "/Wall")

else()

    set(PacBioBAM_CXX_FLAGS "-Wall")

endif()



# NOTE: -Wno-unused-local-typedefs used to quash clang warnings w/ Boost

check_cxx_compiler_flag("-Wno-unused-local-typedefs" HAS_NO_UNUSED_LOCAL_TYPEDEFS)

if(HAS_NO_UNUSED_LOCAL_TYPEDEFS)

    set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-unused-local-typedefs")

endif()



check_cxx_compiler_flag("-Wno-sign-compare" HAS_NO_SIGN_COMPARE)

if(HAS_NO_SIGN_COMPARE)

    set(PacBioBAM_CXX_FLAGS "${PacBioBAM_CXX_FLAGS} -Wno-sign-compare")

endif()



# Turn on windows-style filepath resolution.

# We need to add this #define early (not just in the C# SWIG wrapper)

if(WIN32)

    add_definitions(-DPBBAM_WIN_FILEPATHS)

endif()



# For now, keep @rpath out of install names on OS X, as it causes SWIG

# tests to fail.

if(APPLE)

    set(CMAKE_MACOSX_RPATH OFF)

endif()

cmake/pbbam-dependencies.cmake

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# pthreads

find_package(Threads REQUIRED)



# boost

if(NOT Boost_INCLUDE_DIRS)

    find_package(Boost REQUIRED)

endif()



# Winsock for htslib on Windows

if(WIN32)

    set(SOCKET_LIBRARIES "ws2_32")

endif()



# zlib

if (NOT ZLIB_INCLUDE_DIRS OR NOT ZLIB_LIBRARIES)

    find_package(PkgConfig REQUIRED)

    pkg_check_modules(ZLIB zlib)

    set(ZLIB_LIBRARIES ${ZLIB_LDFLAGS})

else()

    set(ZLIB_LDFLAGS ${ZLIB_LIBRARIES})

endif()



# htslib

if(NOT HTSLIB_INCLUDE_DIRS OR NOT HTSLIB_LIBRARIES)

    find_package(HTSlib)

    set(hts_INCLUDE_DIRS ${HTSlib_INCLUDE_DIRS})

    set(hts_LIBRARIES    ${HTSlib_LIBRARIES})

else()    

    set(hts_INCLUDE_DIRS ${HTSLIB_INCLUDE_DIRS})

    set(hts_LIBRARIES    ${HTSLIB_LIBRARIES})

endif()