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# * Try to find htslib Once done, this will define
#
# htslib_FOUND - system has htslib htslib_INCLUDE_DIRS - the htslib include directories
# htslib_LIBRARIES - link these to use htslib
#
# This code was modified from
# https://github.com/genome/build-common/blob/master/cmake/FindHTSlib.cmake Source:
# https://github.com/luntergroup/octopus/blob/develop/build/cmake/modules/FindHTSlib.cmake
# A simple wrapper to make pkg-config searches a bit easier. Works the same as CMake's internal
# pkg_check_modules but is always quiet.
macro(libfind_pkg_check_modules)
find_package(PkgConfig QUIET)
if(PKG_CONFIG_FOUND)
pkg_check_modules(${ARGN} QUIET)
endif()
endmacro()
macro(libfind_package PREFIX)
set(LIBFIND_PACKAGE_ARGS ${ARGN})
if(${PREFIX}_FIND_QUIETLY)
set(LIBFIND_PACKAGE_ARGS ${LIBFIND_PACKAGE_ARGS} QUIET)
endif(${PREFIX}_FIND_QUIETLY)
if(${PREFIX}_FIND_REQUIRED)
set(LIBFIND_PACKAGE_ARGS ${LIBFIND_PACKAGE_ARGS} REQUIRED)
endif(${PREFIX}_FIND_REQUIRED)
find_package(${LIBFIND_PACKAGE_ARGS})
endmacro(libfind_package)
macro(libfind_process PREFIX)
# Skip processing if already processed during this run
if(NOT ${PREFIX}_FOUND)
# Start with the assumption that the library was found
set(${PREFIX}_FOUND TRUE)
# Process all includes and set _FOUND to false if any are missing
foreach(i ${${PREFIX}_PROCESS_INCLUDES})
if(${i})
set(${PREFIX}_INCLUDE_DIRS ${${PREFIX}_INCLUDE_DIRS} ${${i}})
mark_as_advanced(${i})
else(${i})
set(${PREFIX}_FOUND FALSE)
endif(${i})
endforeach(i)
# Process all libraries and set _FOUND to false if any are missing
foreach(i ${${PREFIX}_PROCESS_LIBS})
if(${i})
set(${PREFIX}_LIBRARIES ${${PREFIX}_LIBRARIES} ${${i}})
mark_as_advanced(${i})
else(${i})
set(${PREFIX}_FOUND FALSE)
endif(${i})
endforeach(i)
# Print message and/or exit on fatal error
if(${PREFIX}_FOUND)
if(NOT ${PREFIX}_FIND_QUIETLY)
message(STATUS "Found ${PREFIX} ${${PREFIX}_VERSION}")
endif(NOT ${PREFIX}_FIND_QUIETLY)
else(${PREFIX}_FOUND)
if(${PREFIX}_FIND_REQUIRED)
foreach(i ${${PREFIX}_PROCESS_INCLUDES} ${${PREFIX}_PROCESS_LIBS})
message("${i}=${${i}}")
endforeach(i)
message(
FATAL_ERROR
"Required library ${PREFIX} NOT FOUND.\nInstall the library (dev version) and try again. If the library is already installed, use ccmake to set the missing variables manually."
)
endif(${PREFIX}_FIND_REQUIRED)
endif(${PREFIX}_FOUND)
endif(NOT ${PREFIX}_FOUND)
endmacro(libfind_process)
set(HTSLIB_SEARCH_DIRS ${HTSLIB_SEARCH_DIRS} $ENV{HTSLIB_ROOT} ${HTSLIB_ROOT})
if(NOT HTSlib_NO_SYSTEM_PATHS)
set(HTSLIB_SEARCH_DIRS ${HTSLIB_SEARCH_DIRS} /usr /usr/local)
endif()
set(_htslib_ver_path "htslib-${htslib_FIND_VERSION}")
# Use pkg-config to get hints about paths
libfind_pkg_check_modules(HTSLIB_PKGCONF htslib)
# Include dir
find_path(
HTSlib_INCLUDE_DIR
NAMES ${HTSLIB_ADDITIONAL_HEADERS} htslib/sam.h
PATHS ${HTSLIB_SEARCH_DIRS} ${HTSLIB_PKGCONF_INCLUDE_DIRS}
PATH_SUFFIXES include htslib/${_htslib_ver_path}
NO_DEFAULT_PATH
)
if(HTSlib_USE_STATIC_LIBS)
# Dependencies
set(ZLIB_ROOT ${HTSLIB_ROOT})
libfind_package(HTSlib ZLIB)
set(BZip2_ROOT ${HTSLIB_ROOT})
libfind_package(HTSlib BZip2)
set(LibLZMA_ROOT ${HTSLIB_ROOT})
libfind_package(HTSlib LibLZMA)
set(CURL_ROOT ${HTSLIB_ROOT})
libfind_package(HTSlib CURL)
if(NOT APPLE)
set(OpenSSL_ROOT ${HTSLIB_ROOT})
libfind_package(HTSlib OpenSSL)
endif()
set(HTSlib_LIBRARY_names libhts.a)
else()
set(HTSlib_LIBRARY_names libhts.so libhts.so.2 libhts.dylib libhts.2.dylib)
endif()
# Finally the library itself
find_library(
HTSlib_LIBRARY
NAMES ${HTSlib_LIBRARY_names}
PATHS ${HTSlib_INCLUDE_DIR} ${HTSLIB_SEARCH_DIRS} ${HTSLIB_PKGCONF_LIBRARY_DIRS}
NO_DEFAULT_PATH
PATH_SUFFIXES lib lib64 lib/x86_64-linux-gnu ${_htslib_ver_path}
)
# Set the include dir variables and the libraries and let libfind_process do the rest. NOTE:
# Singular variables for this library, plural for libraries this lib depends on.
set(HTSlib_PROCESS_INCLUDES HTSlib_INCLUDE_DIR)
set(HTSlib_PROCESS_LIBS HTSlib_LIBRARY)
if(HTSlib_USE_STATIC_LIBS)
set(HTSlib_PROCESS_INCLUDES ${HTSlib_PROCESS_INCLUDES} ZLIB_INCLUDE_DIR BZIP2_INCLUDE_DIR
LIBLZMA_INCLUDE_DIRS CURL_INCLUDE_DIRS
)
set(HTSlib_PROCESS_LIBS ${HTSlib_PROCESS_LIBS} ZLIB_LIBRARIES BZIP2_LIBRARIES LIBLZMA_LIBRARIES
CURL_LIBRARIES
)
if(NOT APPLE)
set(HTSlib_PROCESS_INCLUDES ${HTSlib_PROCESS_INCLUDES} OPENSSL_INCLUDE_DIR)
set(HTSlib_PROCESS_LIBS ${HTSlib_PROCESS_LIBS} OPENSSL_LIBRARIES)
endif()
endif()
libfind_process(HTSlib)
message(STATUS " HTSlib include dirs: ${HTSlib_INCLUDE_DIRS}")
message(STATUS " HTSlib libraries: ${HTSlib_LIBRARIES}")
message(STATUS " HTSLIB FOUND: ${HTSlib_FOUND} ")
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