/
meson.build
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/
meson.build
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# Meson build definition
#
# meson --buildtype [debug|release] [--default-library static] build/
# meson test -C build /
#
# To compile with local git module sources use
#
# meson build -Dprefer_system_deps=false
#
# to build static binary for release
#
# meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release
#
# See also meson_options.txt and contrib/README.md
project('freebayes', ['cpp', 'c'],
version : '1.3.8',
default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
static_build = get_option('static')
# used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp')
cc = meson.get_compiler('cpp')
# fastahack_dep = cc.find_library('libfastahack')
lzma_dep = dependency('liblzma', static: static_build)
thread_dep = dependency('threads', static: static_build)
wfa2lib_dep = cc.find_library('libwfa2')
zlib_dep = dependency('zlib', static: static_build)
if get_option('prefer_system_deps') # defaults to true, otherwise use git modules and local sources
htslib_dep = dependency('htslib', static: static_build, required: false)
seqlib_dep = dependency('libseqlib', static: static_build, required: false)
vcflib_dep = cc.find_library('libvcflib')
fastahack_dep = cc.find_library('libfastahack', required: true)
smithwaterman_dep = cc.find_library('libsmithwaterman')
tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
else
# uses the local git submodules or checkout trees in ./contrib/
# IMPORTANT: this section is untested and broken right now (FIXME)
htslib_dep = dependency('', required : false)
tabixpp_dep = dependency('', required : false)
fastahack_dep = dependency('', required : false)
vcflib_dep = dependency('', required : false)
seqlib_dep = dependency('', required : false)
fastahack_inc = include_directories('contrib/fastahack')
fastahack_src = files(
'contrib/fastahack/Fasta.cpp',
)
multichoose_inc = include_directories('contrib/multichoose')
multichoose_src = files(
)
smithwaterman_inc = include_directories('contrib/smithwaterman')
smithwaterman_src = files(
'contrib/smithwaterman/SmithWatermanGotoh.cpp',
'contrib/smithwaterman/disorder.cpp',
'contrib/smithwaterman/Repeats.cpp',
'contrib/smithwaterman/LeftAlign.cpp',
'contrib/smithwaterman/IndelAllele.cpp',
)
if not tabixpp_dep.found() # tabixpp-dev is in Debian
tabixpp_inc = include_directories('contrib/vcflib/contrib/tabixpp/')
tabixpp_src = files('contrib/vcflib/contrib/tabixpp/tabix.cpp')
tabixpp_lib = static_library('custom_tabixpp',
tabixpp_src,
include_directories : [tabixpp_inc, htslib_inc],
override_options : warn_quiet)
tabixpp_dep = declare_dependency(link_with : tabixpp_lib,
include_directories : tabixpp_inc)
endif
if not htslib_dep.found()
htslib_inc = include_directories(
'contrib/vcflib/contrib/tabixpp/htslib/',
'contrib/htslib_config',
'contrib/vcflib/contrib/tabixpp/htslib/cram',
)
htslib_src = files(
'contrib/vcflib/contrib/tabixpp/htslib/tbx.c', # used by vcflib
'contrib/vcflib/contrib/tabixpp/htslib/bgzf.c',
'contrib/vcflib/contrib/tabixpp/htslib/sam.c',
'contrib/vcflib/contrib/tabixpp/htslib/hts.c',
'contrib/vcflib/contrib/tabixpp/htslib/hfile.c',
'contrib/vcflib/contrib/tabixpp/htslib/textutils.c',
'contrib/vcflib/contrib/tabixpp/htslib/thread_pool.c',
'contrib/vcflib/contrib/tabixpp/htslib/region.c',
'contrib/vcflib/contrib/tabixpp/htslib/hts_os.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_index.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_io.c',
'contrib/vcflib/contrib/tabixpp/htslib/header.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/pooled_alloc.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/string_alloc.c',
'contrib/vcflib/contrib/tabixpp/htslib/md5.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_encode.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_stats.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_codecs.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_decode.c',
'contrib/vcflib/contrib/tabixpp/htslib/kstring.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/cram_external.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/mFILE.c',
'contrib/vcflib/contrib/tabixpp/htslib/faidx.c',
'contrib/vcflib/contrib/tabixpp/htslib/hts_expr.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/rANS_static.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/arith_dynamic.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/fqzcomp_qual.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/htscodecs.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/rANS_static.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/tokenise_name3.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/utils.c',
'contrib/vcflib/contrib/tabixpp/htslib/cram/open_trace_file.c',
'contrib/vcflib/contrib/tabixpp/htslib/multipart.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/rANS_static4x16pr.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/rANS_static32x16pr.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/pack.c',
'contrib/vcflib/contrib/tabixpp/htslib/htscodecs/htscodecs/rle.c',
)
htslib_lib = static_library('custom_htslib',
htslib_src,
include_directories : htslib_inc,
override_options : warn_quiet)
htslib_dep = declare_dependency(link_with : htslib_lib,
include_directories : htslib_inc)
else
htslib_inc = []
endif
vcflib_inc = include_directories()
if not vcflib_dep.found()
vcflib_inc = include_directories(
'contrib/vcflib/src',
'contrib/vcflib/contrib/smithwaterman',
'contrib/vcflib/contrib/multichoose',
'contrib/vcflib/contrib/filevercmp',
'contrib/vcflib/contrib/fastahack',
)
vcflib_src = files(
'contrib/vcflib/src/Variant.cpp',
'contrib/vcflib/src/allele.cpp',
'contrib/vcflib/src/cigar.cpp',
'contrib/vcflib/src/split.cpp',
)
vcflib_lib = static_library('custom_vcflib',
vcflib_src,
include_directories : [htslib_inc, tabixpp_inc, vcflib_inc],
override_options : warn_quiet)
vcflib_dep = declare_dependency(link_with : vcflib_lib,
include_directories : vcflib_inc)
endif
endif # build git modules
# for setting a warning_level on the external code in custom_* targets below
warn_quiet = ['warning_level=0']
if not seqlib_dep.found() # Seqlib is not in Guix (yet) but it is in Debian
seqlib_inc = include_directories(
'contrib/SeqLib',
)
seqlib_src = files(
'contrib/SeqLib/src/BamReader.cpp',
'contrib/SeqLib/src/BamRecord.cpp',
'contrib/SeqLib/src/BamHeader.cpp',
'contrib/SeqLib/src/BamWriter.cpp',
'contrib/SeqLib/src/GenomicRegion.cpp',
'contrib/SeqLib/src/ssw_cpp.cpp',
'contrib/SeqLib/src/ssw.c',
)
seqlib_lib = static_library('custom_seqlib',
seqlib_src,
include_directories : [seqlib_inc],
override_options : warn_quiet)
seqlib_dep = declare_dependency(link_with : seqlib_lib,
include_directories : seqlib_inc)
endif
#
# Sources
#
freebayes_common_src = files(
'src/Allele.cpp',
'src/AlleleParser.cpp',
'src/BedReader.cpp',
'src/Bias.cpp',
'src/CNV.cpp',
'src/Contamination.cpp',
'src/DataLikelihood.cpp',
'src/Dirichlet.cpp',
'src/Ewens.cpp',
'src/FBFasta.cpp',
'src/Genotype.cpp',
'src/IndelAllele.cpp',
'src/LeftAlign.cpp',
'src/Marginals.cpp',
'src/Multinomial.cpp',
'src/NonCall.cpp',
'src/Parameters.cpp',
'src/Result.cpp',
'src/ResultData.cpp',
'src/Sample.cpp',
'src/SegfaultHandler.cpp',
'src/Utility.cpp',
)
freebayes_src = files('src/freebayes.cpp')
bamleftalign_src = files('src/bamleftalign.cpp')
# Include paths
incdir = include_directories(
'src',
'contrib/ttmath',
)
extra_cpp_args = cc.get_supported_arguments(
'-fpermissive',
'-Wno-reorder',
'-Wno-sign-compare',
'-Wno-unused-variable',
'-Wno-unused-but-set-variable',
)
freebayes_lib = static_library(
'freebayes_common',
freebayes_common_src,
include_directories : incdir,
cpp_args : extra_cpp_args,
dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
vcflib_dep, wfa2lib_dep, seqlib_dep],
install : false,
)
if static_build
link_arguments = '-static'
else
link_arguments = []
endif
executable('freebayes',
[freebayes_src],
include_directories : incdir,
cpp_args : extra_cpp_args,
link_args: link_arguments,
dependencies: [zlib_dep,
lzma_dep,
thread_dep,
htslib_dep,
tabixpp_dep,
vcflib_dep,
seqlib_dep,
fastahack_dep, # for vcflib
smithwaterman_dep, # for vcflib
wfa2lib_dep],
link_with : freebayes_lib,
install: true
)
executable('bamleftalign',
[bamleftalign_src],
include_directories : incdir,
cpp_args : extra_cpp_args,
link_args: link_arguments,
dependencies: [zlib_dep,
lzma_dep,
thread_dep,
htslib_dep,
vcflib_dep,
seqlib_dep,
fastahack_dep, # for vcflib
smithwaterman_dep, # for vcflib
wfa2lib_dep],
link_with : freebayes_lib,
install: true
)
testdir = meson.current_source_dir()+'/test'
prove = find_program('prove')
test('T00', prove, args : ['-e','bash','-v','t/00_region_and_target_handling.t'], workdir: testdir)
test('T01', prove, args : ['-e','bash','-v','t/01_call_variants.t'], workdir : testdir )
test('T01b', prove, args : ['-e','bash','-v','t/01b_call_variants.t'], workdir : testdir )
test('T02', prove, args : ['-e','bash','-v','t/02_multi_bam.t'], workdir : testdir )
test('T03', prove, args : ['-e','bash','-v','t/03_reference_bases.t'], workdir: testdir )