1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
|
This patch is original to Guix, ongoing work to upstream bits as possible.
From 50833daba0b1dbe2ed364b1e980b67a09a312789 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 | 60 +++++++++++++++++++++++++++++++++++++++++------------
1 file changed, 47 insertions(+), 13 deletions(-)
diff --git a/meson.build b/meson.build
index f6bf242..7a3805e 100644
--- a/meson.build
+++ b/meson.build
@@ -9,8 +9,12 @@ 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)
thread_dep = dependency('threads')
if htslib_dep.found()
@@ -59,6 +63,41 @@ else
]
endif
+if tabixpp_dep.found()
+ tabixpp_includes = ''
+ tabixpp_src = []
+else
+ tabixpp_includes = [
+ 'vcflib/tabixpp',
+ ]
+ tabixpp_src = [
+ 'vcflib/tabixpp/tabix.cpp',
+ ]
+endif
+
+if fastahack_dep.found()
+ fastahack_src = []
+else
+ fastahack_src = [
+ 'vcflib/fastahack/Fasta.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
#
@@ -105,22 +144,17 @@ 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',
+ 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',
+ fastahack_src,
+ smithwaterman_src,
'vcflib/src/split.cpp',
'src/LeftAlign.cpp',
]
@@ -135,8 +169,8 @@ incdir = include_directories(
'contrib',
'contrib/SeqLib',
'vcflib/src',
- 'vcflib/tabixpp',
- 'vcflib/smithwaterman',
+ tabixpp_includes,
+ smithwaterman_includes,
'vcflib/multichoose',
'vcflib/filevercmp')
@@ -152,7 +186,7 @@ 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, thread_dep],
install: true
)
@@ -165,7 +199,7 @@ 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, thread_dep],
install: true
)
--
2.30.0
|
