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meson.build
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meson.build
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# Sambamba can use meson with:
# source guix-build
# rm -rf build/ ; env D_LD=gold CC=gcc meson build
# cd build/
# env CC=gcc ninja
#
# See also INSTALL.md
project('Sambamba', ['c','d'],
license : 'GPL-2.0',
version : '1.0.1',
# default_options : ['buildtype=debugoptimized']
)
# lang = 'd'
# dc = meson.get_compiler(lang)
source_root = meson.source_root()
build_root = meson.build_root()
# we need a C compiler for the static library search (for BioD) to work,
# as the D compiler abstraction in Meson doesn't have find_library() capabilities yet
cc = meson.get_compiler('c')
if meson.get_compiler('d').get_id() != 'llvm'
error('We only support the LLVM D compiler at this time. Please compile with LDC.')
endif
# The optimized flags are
# ldc2 -singleobj -wi -I. -IBioD -g -J. -O3 -release -enable-inlining -boundscheck=off -L-lz -c -of=bin/sambamba-0.8.2.o
extra_dflags = [ '-I../BioD','-I../BioD/contrib/msgpack-d/src','-g','-release','-boundscheck=off','-enable-inlining','-singleobj']
extra_ldflags = ['-L=-flto=full']
#
# Sources
#
undead_src = [
'BioD/contrib/undead/cstream.d',
'BioD/contrib/undead/doformat.d',
'BioD/contrib/undead/internal/file.d',
'BioD/contrib/undead/stream.d',
'BioD/contrib/undead/utf.d'
]
biod_src = [
'BioD/bio/core/base.d',
'BioD/bio/core/bgzf/block.d',
'BioD/bio/core/bgzf/chunk.d',
'BioD/bio/core/bgzf/compress.d',
'BioD/bio/core/bgzf/constants.d',
'BioD/bio/core/bgzf/inputstream.d',
'BioD/bio/core/bgzf/outputstream.d',
'BioD/bio/core/bgzf/virtualoffset.d',
'BioD/bio/core/call.d',
'BioD/bio/core/decompress.d',
'BioD/bio/core/genotype.d',
'BioD/bio/core/kmer.d',
'BioD/bio/core/region.d',
'BioD/bio/core/sequence.d',
'BioD/bio/core/tinymap.d',
'BioD/bio/core/utils/algo.d',
'BioD/bio/core/utils/bylinefast.d',
'BioD/bio/core/utils/exception.d',
'BioD/bio/core/utils/format.d',
'BioD/bio/core/utils/memoize.d',
'BioD/bio/core/utils/outbuffer.d',
'BioD/bio/core/utils/range.d',
'BioD/bio/core/utils/roundbuf.d',
'BioD/bio/core/utils/stream.d',
'BioD/bio/core/utils/switchendianness.d',
'BioD/bio/core/utils/tmpfile.d',
'BioD/bio/core/utils/zlib.d',
'BioD/bio/std/experimental/hts/bam/header.d',
'BioD/bio/std/experimental/hts/bam/reader.d',
'BioD/bio/std/experimental/hts/bam/writer.d',
'BioD/bio/std/experimental/hts/bgzf.d',
'BioD/bio/std/experimental/hts/bgzf_writer.d',
'BioD/bio/std/experimental/hts/constants.d',
'BioD/bio/std/experimental/hts/hashing.d',
'BioD/bio/std/experimental/hts/logger.d',
'BioD/bio/std/experimental/hts/pileup.d',
'BioD/bio/std/experimental/hts/reads.d',
'BioD/bio/std/experimental/hts/unpack.d',
'BioD/bio/std/file/fai.d',
'BioD/bio/std/file/fasta.d',
'BioD/bio/std/file/fastq.d',
'BioD/bio/std/genotype/maf.d',
'BioD/bio/std/genotype/snp.d',
'BioD/bio/std/hts/bam/abstractreader.d',
'BioD/bio/std/hts/bam/bai/bin.d',
'BioD/bio/std/hts/bam/baifile.d',
'BioD/bio/std/hts/bam/bai/indexing.d',
'BioD/bio/std/hts/bam/baseinfo.d',
'BioD/bio/std/hts/bam/cigar.d',
'BioD/bio/std/hts/bam/constants.d',
'BioD/bio/std/hts/bam/md/core.d',
'BioD/bio/std/hts/bam/md/operation.d',
'BioD/bio/std/hts/bam/md/parse.d',
'BioD/bio/std/hts/bam/md/reconstruct.d',
'BioD/bio/std/hts/bam/multireader.d',
'BioD/bio/std/hts/bam/pileup.d',
'BioD/bio/std/hts/bam/randomaccessmanager.d',
'BioD/bio/std/hts/bam/read.d',
'BioD/bio/std/hts/bam/reader.d',
'BioD/bio/std/hts/bam/readrange.d',
'BioD/bio/std/hts/bam/reference.d',
'BioD/bio/std/hts/bam/referenceinfo.d',
'BioD/bio/std/hts/bam/region.d',
'BioD/bio/std/hts/bam/splitter.d',
'BioD/bio/std/hts/bam/tagvalue.d',
'BioD/bio/std/hts/bam/validation/alignment.d',
'BioD/bio/std/hts/bam/validation/samheader.d',
'BioD/bio/std/hts/bam/writer.d',
'BioD/bio/std/hts/iontorrent/flowcall.d',
'BioD/bio/std/hts/iontorrent/flowindex.d',
'BioD/bio/std/hts/sam/header.d',
'BioD/bio/std/hts/sam/reader.d',
'BioD/bio/std/hts/sam/utils/fastrecordparser.d',
'BioD/bio/std/hts/sam/utils/recordparser.d',
'BioD/bio/std/hts/snpcallers/maq.d',
'BioD/bio/std/hts/snpcallers/simple.d',
'BioD/bio/std/hts/utils/array.d',
'BioD/bio/std/hts/utils/graph.d',
'BioD/bio/std/hts/utils/samheadermerger.d',
'BioD/bio/std/hts/utils/value.d',
'BioD/bio/std/maf/block.d',
'BioD/bio/std/maf/parser.d',
'BioD/bio/std/maf/reader.d',
'BioD/bio/std/range/splitter.d',
'BioD/bio/std/sff/constants.d',
'BioD/bio/std/sff/index.d',
'BioD/bio/std/sff/read.d',
'BioD/bio/std/sff/reader.d',
'BioD/bio/std/sff/readrange.d',
'BioD/bio/std/sff/utils/roundup.d',
'BioD/bio/std/sff/writer.d'
]
sambamba_src = [
'sambamba/depth.d',
'sambamba/fixbins.d',
'sambamba/flagstat.d',
'sambamba/index.d',
'sambamba/markdup2.d',
'sambamba/markdup.d',
'sambamba/merge.d',
'sambamba/pileup.d',
'sambamba/slice.d',
'sambamba/sort.d',
'sambamba/subsample.d',
'sambamba/utils/common/bed.d',
'sambamba/utils/common/file.d',
'sambamba/utils/common/filtering.d',
'sambamba/utils/common/intervaltree.d',
'sambamba/utils/common/ldc_gc_workaround.d',
'sambamba/utils/common/overwrite.d',
'sambamba/utils/common/pratt_parser.d',
'sambamba/utils/common/progressbar.d',
'sambamba/utils/common/queryparser.d',
'sambamba/utils/common/readstorage.d',
'sambamba/utils/common/tmpdir.d',
'sambamba/utils/view/alignmentrangeprocessor.d',
'sambamba/utils/view/headerserializer.d',
'sambamba/validate.d',
'sambamba/view.d',
]
utils_src = [
'utils/lz4.d',
'utils/strip_bcf_header.d',
'utils/version_.d'
]
cram_src = [
]
thirdparty_src = [
'thirdparty/mergesort.d',
'thirdparty/unstablesort.d',
'BioD/contrib/msgpack-d/src/msgpack/attribute.d',
'BioD/contrib/msgpack-d/src/msgpack/common.d',
'BioD/contrib/msgpack-d/src/msgpack/package.d',
'BioD/contrib/msgpack-d/src/msgpack/register.d',
'BioD/contrib/msgpack-d/src/msgpack/unpacker.d',
'BioD/contrib/msgpack-d/src/msgpack/buffer.d',
'BioD/contrib/msgpack-d/src/msgpack/exception.d',
'BioD/contrib/msgpack-d/src/msgpack/packer.d',
'BioD/contrib/msgpack-d/src/msgpack/streaming_unpacker.d',
'BioD/contrib/msgpack-d/src/msgpack/value.d',
]
manpages = [
'man/sambamba.1',
'man/sambamba-flagstat.1',
'man/sambamba-index.1',
'man/sambamba-markdup.1',
'man/sambamba-merge.1',
'man/sambamba-pileup.1',
'man/sambamba-slice.1',
'man/sambamba-sort.1',
'man/sambamba-view.1'
]
#
# Dependencies
#
lz4 = dependency('liblz4')
zlib = dependency('zlib')
#
# Configure
#
# Write LDC version to file
ldmd_prog = find_program('ldc2')
mkdir_prog = find_program('mkdir')
r = run_command(mkdir_prog.path(), '-p', build_root + '/utils/')
if r.returncode() != 0
error('Unable to create "utils/" directory in build root: ' + r.stderr().strip())
endif
version_info_d_fname = build_root + '/utils/ldc_version_info_.d'
r = run_command('python3', source_root + '/gen_ldc_version_info.py', ldmd_prog.path(), version_info_d_fname)
if r.returncode() != 0
error('Unable to write LDC version file: ' + r.stderr().strip())
endif
#
# Targets
#
sambamba_exe = executable('sambamba',
['sambamba/main.d',
sambamba_src,
biod_src,
undead_src,
utils_src,
cram_src,
thirdparty_src,
version_info_d_fname],
dependencies: [zlib,lz4],
d_args: extra_dflags,
link_args: extra_ldflags,
d_import_dirs: [include_directories('.'),include_directories('BioD')],
install: true
)
test_exe = find_program(join_paths(source_root, 'test', 'test_suite.sh'))
test('sambamba_test',test_exe,
args: sambamba_exe.full_path(),
workdir: source_root
)
#
# Install extra files
#
install_man(manpages)
install_data(['etc/bash_completion.d/sambamba'], install_dir: '/usr/share/bash-completion/completions')