project('libdna', 'c', 'cpp',

version : '1.3',

license : 'MIT',

default_options : ['warning_level=3', 'c_std=gnu11', 'cpp_std=c++17',

'b_ndebug=if-release', 'buildtype=release']

)

cc = meson.get_compiler('c')

aversion = meson.project_version().split('.')

major = aversion[0].to_int()

minor = aversion[1].to_int()

configure_file(

input: 'src/config.h.in',

output: 'config.h',

configuration: {

'CAN_IFUNC': cc.has_function_attribute('ifunc').to_int(),

'CAN_CONSTRUCTOR': cc.has_function_attribute('constructor').to_int(),

'MINOR': minor,

'MAJOR': major

}

)

has_native = cc.has_argument('-march=native')

native_flag = has_native ? '-march=native' : ''

incdir = include_directories('include', 'bench', 'test', 'src')

genericfiles = [

'src/dna4_count_mismatches_rc.c',

'src/dna4_fill_random.c',

'src/dna4_pack_2bits.c',

'src/dna4_revcomp.c',

'src/dna4_unpack_2bits.c',

'src/dna_ihash.c',

'src/dna_ihash_invert.c',

'src/dna_internal.h',

'src/dna_version.c',

'src/dnax_count.c',

'src/dnax_count_mismatches.c',

'src/dnax_extract_dna4.c',

'src/dnax_find_first_mismatch.c',

'src/dnax_find_first_not_of.c',

'src/dnax_find_first_of.c',

'src/dnax_pack_4bits.c',

'src/dnax_replace.c',

'src/dnax_revcomp.c',

'src/dnax_tables.c',

'src/dnax_translate.c',

'src/dnax_unpack_4bits.c',

'src/utils.h'

]

isaspecificlibs = []

if host_machine.cpu_family() == 'x86_64'

genericfiles += [

'src/dna4_count_mismatches_rc_x86.c',

'src/dna4_fill_random_x86.c',

'src/dna4_revcomp_x86.c',

'src/dnax_count_mismatches_x86.c',

'src/dnax_extract_dna4_x86.c'

]

sse42files = [

'src/dna4_count_mismatches_rc_sse42.c',

'src/dna4_fill_random_sse42.c',

'src/dna4_revcomp_sse42.c',

'src/dnax_count_mismatches_sse42.c',

'src/dnax_extract_dna4_sse42.c'

]

sse42lib = static_library('sse42lib', sse42files,

include_directories: incdir,

pic: true,

c_args : ['-O3', '-mpopcnt', '-msse4.2', '-fvisibility=hidden']

)

avx2files = [

'src/dna4_count_mismatches_rc_avx2.c',

'src/dna4_fill_random_avx2.c',

'src/dna4_revcomp_avx2.c',

'src/dnax_count_mismatches_avx2.c'

]

avx2lib = static_library('avx2lib', avx2files,

include_directories: incdir,

pic: true,

c_args : ['-O3', '-mpopcnt', '-mavx2', '-fvisibility=hidden']

)

avx512files = ['src/dnax_count_mismatches_avx512.c']

avx512lib = static_library('avx512lib', avx512files,

include_directories: incdir,

pic: true,

c_args : ['-O3', '-mpopcnt', '-mavx512bw', '-mavx512vl', '-fvisibility=hidden']

)

isaspecificlibs = [sse42lib, avx2lib, avx512lib]

if host_machine.cpu_family() == 'aarch64'

neonfiles = ['src/dna4_revcomp_neon.c', 'src/dnax_count_mismatches_neon.c']

neonlib = static_library('neonlib', neonfiles,

include_directories: incdir,

pic: true,

c_args : ['-O3', '-fvisibility=hidden']

)

isaspecificlibs = [neonlib]

libdna = library('dna', ['include/dna.h', genericfiles],

include_directories : incdir,

soversion: '0',

link_whole: isaspecificlibs,

pic: true,

c_args : ['-O2', '-fvisibility=hidden', '-Wno-overlength-strings'],

install: true

)

install_headers('include/dna.h', 'include/dna.hpp', subdir: 'kloetzl')

install_man([

'man/dna4_count_mismatches_rc.3',

'man/dna4_fill_random.3',

'man/dna4_pack_2bits.3',

'man/dna4_revcomp.3',

'man/dna4_unpack_2bits.3',

'man/dna_ihash.3',

'man/dna_ihash_invert.3',

'man/dnax_count.3',

'man/dnax_count_mismatches.3',

'man/dnax_extract_dna4.3',

'man/dnax_find_first_mismatch.3',

'man/dnax_find_first_not_of.3',

'man/dnax_find_first_of.3',

'man/dnax_pack_4bits.3',

'man/dnax_replace.3',

'man/dnax_revcomp.3',

'man/dnax_translate.3',

'man/dnax_unpack_4bits.3',

'man/geneticcode.7',

'man/iupac.7'

])

libdna_dep = declare_dependency(include_directories : 'include',

link_with : libdna)

pkg = import('pkgconfig')

pkg.generate(

libraries : libdna,

subdirs : ['.', 'kloetzl'],

name : 'libdna',

description : 'Essential Functions for DNA Manipulation'

)

if get_option('with-tests')

catch2_dep = dependency('catch2', fallback: ['catch2', 'catch2_dep'])

testlib = static_library('Tmain', 'test/Tmain.cxx',

include_directories: incdir,

cpp_args : ['-O2'],

install: false,

dependencies: catch2_dep

)

nativetests = ['Tifunc']

foreach Tname : nativetests

Texe = executable(Tname,

'test/' + Tname + '.cxx',

link_with: [testlib, libdna],

install: false,

build_by_default: false,

include_directories: incdir,

cpp_args: [native_flag],

dependencies: catch2_dep

)

test(Tname, Texe)

endforeach

plaintests = [

'Tcompare',

'Tcount_mismatches_rc',

'Tdna4_pack_2bits',

'Tdna4_revcomp',

'Tdnax_extract_dna4',

'Tdnax_pack_4bits',

'Tdnax_revcomp',

'Tihash',

'Tfill_random',

'Tsimple',

'Ttranslate'

]

foreach Tname : plaintests

Texe = executable(Tname,

'test/' + Tname + '.cxx',

link_with: [testlib, libdna],

install: false,

build_by_default: false,

include_directories: incdir,

dependencies: catch2_dep

)

test(Tname, Texe)

endforeach

examples = {

'edit_distance': 'edit_distance.cxx',

'fasta': 'fasta.c',

'gc_content': 'gc_content.cxx',

'geneticcode_table': 'geneticcode_table.cxx',

'kasai': 'kasai.c',

'randomseq': 'random.c'

}

foreach example, file_name : examples

exe = executable(example,

'examples/' + file_name,

link_with: [libdna],

install: false,

build_by_default: false,

include_directories: incdir

)

test(example, exe)

endforeach

if get_option('with-benchmarks')

benchcommonlib = static_library('benchcommon', 'bench/Bcommon.cxx',

include_directories: incdir,

cpp_args : ['-O2'],

install: false

)

libbenchmark = dependency('benchmark',

fallback: ['google-benchmark', 'google_benchmark_dep'])

plainbench = [

'Bcompare',

'Bcompare_rev',

'Bcompare_wg',

'Bfill_random',

'Bmismatch',

'Bpack',

'Brevcomp',

'Bstrconstr',

'Btranslate'

]

foreach Bname : plainbench

Bexe = executable(Bname, 'bench/' + Bname + '.cxx',

link_with: [libdna, benchcommonlib],

install: false,

build_by_default: true,

include_directories: incdir,

dependencies: libbenchmark,

cpp_args: ['-Ofast', native_flag]

)

benchmark(Bname, Bexe)

endforeach

Bdnax_to_dna4 = executable('Bdnax_to_dna4', 'bench/Bdnax_to_dna4.cxx', 'bench/despace_tables.h',

link_with: [libdna, benchcommonlib],

install: false,

build_by_default: true,

include_directories: incdir,

dependencies: libbenchmark,

cpp_args: ['-Ofast', native_flag]

)

benchmark('Bdnax_to_dna4', Bdnax_to_dna4)