set(CPM_DOWNLOAD_VERSION 0.32.3) set(CPM_DOWNLOAD_LOCATION "${CMAKE_BINARY_DIR}/cmake/CPM_${CPM_DOWNLOAD_VERSION}.cmake") if(NOT (EXISTS ${CPM_DOWNLOAD_LOCATION})) message(STATUS "Downloading CPM.cmake...") file(DOWNLOAD https://github.com/TheLartians/CPM.cmake/releases/download/v${CPM_DOWNLOAD_VERSION}/CPM.cmake ${CPM_DOWNLOAD_LOCATION}) endif() include(${CPM_DOWNLOAD_LOCATION}) CPMAddPackage( NAME zlibng GITHUB_REPOSITORY "zlib-ng/zlib-ng" VERSION 2.0.5 GIT_TAG 2.0.5 OPTIONS "HAVE_OFF64_T ON" "ZLIB_COMPAT ON" "ZLIB_ENABLE_TESTS OFF" "CMAKE_POSITION_INDEPENDENT_CODE ON") set_target_properties(zlib PROPERTIES EXCLUDE_FROM_ALL ON) CPMAddPackage( NAME xz GIT_REPOSITORY "https://git.tukaani.org/xz.git" VERSION 5.2.5 OPTIONS "BUILD_SHARED_LIBS OFF" "CMAKE_POSITION_INDEPENDENT_CODE ON") set_target_properties(xz PROPERTIES EXCLUDE_FROM_ALL ON) set_target_properties(xzdec PROPERTIES EXCLUDE_FROM_ALL ON) CPMAddPackage( NAME bdwgc GITHUB_REPOSITORY "ivmai/bdwgc" VERSION 8.0.5 GIT_TAG d0ba209660ea8c663e06d9a68332ba5f42da54ba OPTIONS "CMAKE_POSITION_INDEPENDENT_CODE ON" "BUILD_SHARED_LIBS OFF" "enable_threads ON" "enable_large_config ON" "enable_thread_local_alloc ON" "enable_handle_fork ON") set_target_properties(cord PROPERTIES EXCLUDE_FROM_ALL ON) CPMAddPackage( NAME openmp GITHUB_REPOSITORY "llvm-mirror/openmp" VERSION 9.0 GIT_TAG release_90 OPTIONS "OPENMP_ENABLE_LIBOMPTARGET OFF" "OPENMP_STANDALONE_BUILD ON") CPMAddPackage( NAME backtrace GITHUB_REPOSITORY "ianlancetaylor/libbacktrace" GIT_TAG d0f5e95a87a4d3e0a1ed6c069b5dae7cbab3ed2a DOWNLOAD_ONLY YES) if(backtrace_ADDED) # https://go.googlesource.com/gollvm/+/refs/heads/master/cmake/modules/LibbacktraceUtils.cmake set(BACKTRACE_ELF_SIZE 64) set(HAVE_GETIPINFO 1) set(BACKTRACE_USES_MALLOC 0) set(BACKTRACE_SUPPORTS_THREADS 1) set(BACKTRACE_SUPPORTS_DATA 1) if(HAVE_SYNC_BOOL_COMPARE_AND_SWAP_4) if(HAVE_SYNC_BOOL_COMPARE_AND_SWAP_8) set(HAVE_SYNC_FUNCTIONS 1) endif() endif() # Generate backtrace-supported.h based on the above. configure_file( ${CMAKE_SOURCE_DIR}/scripts/backtrace-supported.h.cmake ${backtrace_SOURCE_DIR}/backtrace-supported.h) configure_file( ${CMAKE_SOURCE_DIR}/scripts/backtrace-config.h.cmake ${backtrace_SOURCE_DIR}/config.h) add_library(backtrace STATIC "${backtrace_SOURCE_DIR}/atomic.c" "${backtrace_SOURCE_DIR}/backtrace.c" "${backtrace_SOURCE_DIR}/dwarf.c" "${backtrace_SOURCE_DIR}/elf.c" "${backtrace_SOURCE_DIR}/fileline.c" "${backtrace_SOURCE_DIR}/mmapio.c" "${backtrace_SOURCE_DIR}/mmap.c" "${backtrace_SOURCE_DIR}/posix.c" "${backtrace_SOURCE_DIR}/print.c" "${backtrace_SOURCE_DIR}/simple.c" "${backtrace_SOURCE_DIR}/sort.c" "${backtrace_SOURCE_DIR}/state.c") target_include_directories(backtrace BEFORE PRIVATE "${backtrace_SOURCE_DIR}") set_target_properties(backtrace PROPERTIES COMPILE_FLAGS "-funwind-tables -D_GNU_SOURCE" POSITION_INDEPENDENT_CODE ON) endif() CPMAddPackage( NAME bz2 URL "https://www.sourceware.org/pub/bzip2/bzip2-1.0.8.tar.gz" DOWNLOAD_ONLY YES) if(bz2_ADDED) add_library(bz2 STATIC "${bz2_SOURCE_DIR}/blocksort.c" "${bz2_SOURCE_DIR}/huffman.c" "${bz2_SOURCE_DIR}/crctable.c" "${bz2_SOURCE_DIR}/randtable.c" "${bz2_SOURCE_DIR}/compress.c" "${bz2_SOURCE_DIR}/decompress.c" "${bz2_SOURCE_DIR}/bzlib.c" "${bz2_SOURCE_DIR}/libbz2.def") set_target_properties(bz2 PROPERTIES COMPILE_FLAGS "-D_FILE_OFFSET_BITS=64" POSITION_INDEPENDENT_CODE ON) endif() CPMAddPackage( NAME htslib VERSION 1.13 URL "https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2" DOWNLOAD_ONLY YES) if(htslib_ADDED) configure_file( ${CMAKE_SOURCE_DIR}/scripts/htslib-config.h.cmake ${htslib_SOURCE_DIR}/config.h COPYONLY) write_file(${htslib_SOURCE_DIR}/version.h "#define HTS_VERSION_TEXT \"${CPM_PACKAGE_htslib_VERSION}\"") write_file(${htslib_SOURCE_DIR}/config_vars.h "#define HTS_CC \"\"\n" "#define HTS_CPPFLAGS \"\"\n" "#define HTS_CFLAGS \"\"\n" "#define HTS_LDFLAGS \"\"\n" "#define HTS_LIBS \"\"\n") add_library(htslib STATIC "${htslib_SOURCE_DIR}/kfunc.c" "${htslib_SOURCE_DIR}/kstring.c" "${htslib_SOURCE_DIR}/bcf_sr_sort.c" "${htslib_SOURCE_DIR}/bgzf.c" "${htslib_SOURCE_DIR}/errmod.c" "${htslib_SOURCE_DIR}/faidx.c" "${htslib_SOURCE_DIR}/header.c" "${htslib_SOURCE_DIR}/hfile.c" "${htslib_SOURCE_DIR}/hts.c" "${htslib_SOURCE_DIR}/hts_expr.c" "${htslib_SOURCE_DIR}/hts_os.c" "${htslib_SOURCE_DIR}/md5.c" "${htslib_SOURCE_DIR}/multipart.c" "${htslib_SOURCE_DIR}/probaln.c" "${htslib_SOURCE_DIR}/realn.c" "${htslib_SOURCE_DIR}/regidx.c" "${htslib_SOURCE_DIR}/region.c" "${htslib_SOURCE_DIR}/sam.c" "${htslib_SOURCE_DIR}/synced_bcf_reader.c" "${htslib_SOURCE_DIR}/vcf_sweep.c" "${htslib_SOURCE_DIR}/tbx.c" "${htslib_SOURCE_DIR}/textutils.c" "${htslib_SOURCE_DIR}/thread_pool.c" "${htslib_SOURCE_DIR}/vcf.c" "${htslib_SOURCE_DIR}/vcfutils.c" "${htslib_SOURCE_DIR}/cram/cram_codecs.c" "${htslib_SOURCE_DIR}/cram/cram_decode.c" "${htslib_SOURCE_DIR}/cram/cram_encode.c" "${htslib_SOURCE_DIR}/cram/cram_external.c" "${htslib_SOURCE_DIR}/cram/cram_index.c" "${htslib_SOURCE_DIR}/cram/cram_io.c" "${htslib_SOURCE_DIR}/cram/cram_stats.c" "${htslib_SOURCE_DIR}/cram/mFILE.c" "${htslib_SOURCE_DIR}/cram/open_trace_file.c" "${htslib_SOURCE_DIR}/cram/pooled_alloc.c" "${htslib_SOURCE_DIR}/cram/string_alloc.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/arith_dynamic.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/fqzcomp_qual.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/htscodecs.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/pack.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/rANS_static4x16pr.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/rANS_static.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/rle.c" "${htslib_SOURCE_DIR}/htscodecs/htscodecs/tokenise_name3.c") target_include_directories(htslib BEFORE PRIVATE "${htslib_SOURCE_DIR}" "${bz2_SOURCE_DIR}" "${xz_SOURCE_DIR}/src/liblzma/api") set_target_properties(htslib PROPERTIES POSITION_INDEPENDENT_CODE ON VISIBILITY_INLINES_HIDDEN ON) endif()