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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 /
#
# Meson builds with locally installed htslib, vcflib, tabixpp and seqlib.
# If one is missing it should pick up the sources from git submodules.
#
# to compile htslib with local sources use
#
# meson build -Dprefer_system_deps=false
#
# to build static binary for release
#
# meson build -Dstatic=true -Dprefer_system_deps=false --buildtype release
project('freebayes', ['cpp', 'c'],
version : '1.3.6',
default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3'])
static_build = get_option('static')
cc = meson.get_compiler('cpp')
zlib_dep = dependency('zlib', static: static_build)
lzma_dep = dependency('liblzma', static: static_build)
thread_dep = dependency('threads', static: static_build)
tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
# to compile htslib use
# meson build -Dprefer_system_deps=false
# otherwise it tries to pick up the local system libs
if get_option('prefer_system_deps')
htslib_dep = dependency('htslib', static: static_build, required: false)
tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false)
vcflib_dep = dependency('libvcflib', static: static_build, required: false)
seqlib_dep = dependency('libseqlib', static: static_build, required: false)
else
# uses the local git submodules
htslib_dep = dependency('', required : false)
tabixpp_dep = dependency('', required : false)
vcflib_dep = dependency('', required : false)
seqlib_dep = dependency('', required : false)
endif
# for setting a warning_level on the external code in custom_* targets below
warn_quiet = ['warning_level=0']
# optionally build from source
# note that the build version adds support for lzma and bzip2 in CRAM
if not htslib_dep.found()
htslib_inc = include_directories(
'contrib/htslib',
'contrib/htslib_config',
'contrib/htslib/cram',
)
htslib_src = files(
'contrib/htslib/tbx.c', # used by vcflib
'contrib/htslib/bgzf.c',
'contrib/htslib/sam.c',
'contrib/htslib/hts.c',
'contrib/htslib/hfile.c',
# 'contrib/htslib/hfile_net.c',
# 'contrib/htslib/knetfile.c',
'contrib/htslib/textutils.c',
'contrib/htslib/thread_pool.c',
'contrib/htslib/region.c',
'contrib/htslib/hts_os.c',
'contrib/htslib/cram/cram_index.c',
'contrib/htslib/cram/cram_io.c',
# the older 'contrib/htslib/cram/sam_header.c', was renamed to
'contrib/htslib/header.c',
'contrib/htslib/cram/pooled_alloc.c',
'contrib/htslib/cram/string_alloc.c',
'contrib/htslib/md5.c',
'contrib/htslib/cram/cram_encode.c',
'contrib/htslib/cram/cram_stats.c',
'contrib/htslib/cram/cram_codecs.c',
'contrib/htslib/cram/cram_decode.c',
# 'contrib/htslib/cram/cram_samtools.c',
'contrib/htslib/kstring.c',
'contrib/htslib/cram/cram_external.c',
# 'contrib/htslib/cram/files.c',
'contrib/htslib/cram/mFILE.c',
'contrib/htslib/faidx.c',
'contrib/htslib/hts_expr.c',
'contrib/htslib/htscodecs/htscodecs/rANS_static.c',
'contrib/htslib/htscodecs/htscodecs/arith_dynamic.c',
'contrib/htslib/htscodecs/htscodecs/fqzcomp_qual.c',
'contrib/htslib/htscodecs/htscodecs/htscodecs.c',
'contrib/htslib/htscodecs/htscodecs/rANS_static.c',
'contrib/htslib/htscodecs/htscodecs/tokenise_name3.c',
'contrib/htslib/cram/open_trace_file.c',
'contrib/htslib/multipart.c',
'contrib/htslib/htscodecs/htscodecs/rANS_static4x16pr.c',
'contrib/htslib/htscodecs/htscodecs/pack.c',
'contrib/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
if not tabixpp_dep.found()
tabixpp_inc = include_directories('vcflib/tabixpp')
tabixpp_src = files('vcflib/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)
else
tabixpp_inc = []
endif
if not vcflib_dep.found()
vcflib_inc = include_directories(
'vcflib/src',
'vcflib/smithwaterman',
'vcflib/multichoose',
'vcflib/filevercmp',
'vcflib/fastahack',
)
vcflib_src = files(
'vcflib/src/Variant.cpp',
'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
'vcflib/smithwaterman/disorder.cpp',
'vcflib/smithwaterman/Repeats.cpp',
'vcflib/smithwaterman/LeftAlign.cpp',
'vcflib/smithwaterman/IndelAllele.cpp',
'vcflib/fastahack/Fasta.cpp',
'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
if not seqlib_dep.found()
seqlib_inc = include_directories(
'contrib',
'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 : [htslib_inc, vcflib_inc, 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',
'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, 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],
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],
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 )