153 lines
4.0 KiB
Diff
153 lines
4.0 KiB
Diff
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
|
|
|