This patch is original to Guix, ongoing work to upstream bits as possible.
From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 17 Jan 2021 13:27:17 +0200
Subject: [PATCH] devendor-dependants
---
meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------
1 file changed, 66 insertions(+), 18 deletions(-)
diff --git a/meson.build b/meson.build
index f6bf242..bded4af 100644
--- a/meson.build
+++ b/meson.build
@@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'],
zlib_dep = dependency('zlib')
lzma_dep = dependency('liblzma')
+simde_dep = dependency('simde')
bzip2_dep = dependency('bz2lib', required: false)
htslib_dep = dependency('htslib', required : false)
+tabixpp_dep = dependency('tabixpp', required : false)
+fastahack_dep = dependency('fastahack', required : false)
+smithwaterman_dep = dependency('smithwaterman', required : false)
+vcflib_dep = dependency('vcflib', required: false)
thread_dep = dependency('threads')
if htslib_dep.found()
@@ -59,6 +64,56 @@ else
]
endif
+if tabixpp_dep.found()
+ tabixpp_includes = ''
+ tabixpp_src = []
+else
+ tabixpp_includes = [
+ 'vcflib/tabixpp',
+ ]
+ tabixpp_src = [
+ 'vcflib/tabixpp/tabix.cpp',
+ ]
+endif
+
+if vcflib_dep.found()
+ vcflib_includes = ''
+ vcflib_src = []
+else
+ vcflib_includes = [
+ 'vcflib/src',
+ 'vcflib/multichoose',
+ 'vcflib/filevercmp',
+ ]
+ vcflib_src = [
+ 'vcflib/src/Variant.cpp',
+ ]
+endif
+
+if fastahack_dep.found()
+ fastahack_src = []
+else
+ fastahack_src = [
+ 'vcflib/fastahack/Fasta.cpp',
+ 'vcflib/src/split.cpp',
+ ]
+endif
+
+if smithwaterman_dep.found()
+ smithwaterman_includes = ''
+ smithwaterman_src = []
+else
+ smithwaterman_includes = [
+ 'vcflib/smithwaterman',
+ ]
+ smithwaterman_src = [
+ 'vcflib/smithwaterman/SmithWatermanGotoh.cpp',
+ 'vcflib/smithwaterman/disorder.cpp',
+ 'vcflib/smithwaterman/Repeats.cpp',
+ 'vcflib/smithwaterman/LeftAlign.cpp',
+ 'vcflib/smithwaterman/IndelAllele.cpp',
+ ]
+endif
#
@@ -105,23 +160,18 @@ seqlib_src = [
]
vcflib_src = [
- 'vcflib/tabixpp/tabix.cpp',
- '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_src,
+ tabixpp_src,
+ smithwaterman_src,
]
bamleftalign_src = [
'src/bamleftalign.cpp',
'src/IndelAllele.cpp',
'contrib/SeqLib/src/BamWriter.cpp',
- 'vcflib/fastahack/Fasta.cpp',
- 'vcflib/smithwaterman/LeftAlign.cpp',
- 'vcflib/smithwaterman/IndelAllele.cpp',
- 'vcflib/src/split.cpp',
+ fastahack_src,
+ smithwaterman_src,
+ vcflib_src,
'src/LeftAlign.cpp',
]
@@ -134,11 +184,9 @@ incdir = include_directories(
'ttmath',
'contrib',
'contrib/SeqLib',
- 'vcflib/src',
- 'vcflib/tabixpp',
- 'vcflib/smithwaterman',
- 'vcflib/multichoose',
- 'vcflib/filevercmp')
+ tabixpp_includes,
+ smithwaterman_includes,
+ vcflib_includes)
c_args = ['-fpermissive','-w']
cpp_args = ['-fpermissive','-w','-Wc++14-compat']
@@ -152,7 +200,7 @@ executable('freebayes',
include_directories : incdir,
cpp_args : cpp_args,
c_args : c_args,
- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep],
install: true
)
@@ -165,7 +213,7 @@ executable('bamleftalign',
include_directories : incdir,
cpp_args : cpp_args,
c_args : c_args,
- dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep],
+ dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep],
install: true
)
--
2.30.0