Commit | Line | Data |
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1 | This patch is original to Guix, ongoing work to upstream bits as possible. |
2 | ||
99043adf | 3 | From 9acc56db5e7469f5976be38b52ba4993de98ee38 Mon Sep 17 00:00:00 2001 |
fc9fd549 EF |
4 | From: Efraim Flashner <efraim@flashner.co.il> |
5 | Date: Sun, 17 Jan 2021 13:27:17 +0200 | |
6 | Subject: [PATCH] devendor-dependants | |
7 | ||
8 | --- | |
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9 | meson.build | 84 +++++++++++++++++++++++++++++++++++++++++------------ |
10 | 1 file changed, 66 insertions(+), 18 deletions(-) | |
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11 | |
12 | diff --git a/meson.build b/meson.build | |
99043adf | 13 | index f6bf242..bded4af 100644 |
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14 | --- a/meson.build |
15 | +++ b/meson.build | |
99043adf | 16 | @@ -9,8 +9,13 @@ project('freebayes', ['cpp', 'c'], |
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17 | |
18 | zlib_dep = dependency('zlib') | |
19 | lzma_dep = dependency('liblzma') | |
20 | +simde_dep = dependency('simde') | |
21 | bzip2_dep = dependency('bz2lib', required: false) | |
22 | htslib_dep = dependency('htslib', required : false) | |
23 | +tabixpp_dep = dependency('tabixpp', required : false) | |
24 | +fastahack_dep = dependency('fastahack', required : false) | |
25 | +smithwaterman_dep = dependency('smithwaterman', required : false) | |
877ab026 | 26 | +vcflib_dep = dependency('vcflib', required: false) |
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27 | thread_dep = dependency('threads') |
28 | ||
29 | if htslib_dep.found() | |
99043adf | 30 | @@ -59,6 +64,56 @@ else |
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31 | ] |
32 | endif | |
33 | ||
34 | +if tabixpp_dep.found() | |
35 | + tabixpp_includes = '' | |
36 | + tabixpp_src = [] | |
37 | +else | |
38 | + tabixpp_includes = [ | |
39 | + 'vcflib/tabixpp', | |
40 | + ] | |
41 | + tabixpp_src = [ | |
42 | + 'vcflib/tabixpp/tabix.cpp', | |
43 | + ] | |
44 | +endif | |
45 | + | |
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46 | +if vcflib_dep.found() |
47 | + vcflib_includes = '' | |
48 | + vcflib_src = [] | |
49 | +else | |
50 | + vcflib_includes = [ | |
51 | + 'vcflib/src', | |
52 | + 'vcflib/multichoose', | |
53 | + 'vcflib/filevercmp', | |
54 | + ] | |
55 | + vcflib_src = [ | |
56 | + 'vcflib/src/Variant.cpp', | |
57 | + ] | |
58 | +endif | |
59 | + | |
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60 | +if fastahack_dep.found() |
61 | + fastahack_src = [] | |
62 | +else | |
63 | + fastahack_src = [ | |
64 | + 'vcflib/fastahack/Fasta.cpp', | |
99043adf | 65 | + 'vcflib/src/split.cpp', |
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66 | + ] |
67 | +endif | |
68 | + | |
69 | +if smithwaterman_dep.found() | |
70 | + smithwaterman_includes = '' | |
71 | + smithwaterman_src = [] | |
72 | +else | |
73 | + smithwaterman_includes = [ | |
74 | + 'vcflib/smithwaterman', | |
75 | + ] | |
76 | + smithwaterman_src = [ | |
77 | + 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', | |
78 | + 'vcflib/smithwaterman/disorder.cpp', | |
79 | + 'vcflib/smithwaterman/Repeats.cpp', | |
80 | + 'vcflib/smithwaterman/LeftAlign.cpp', | |
81 | + 'vcflib/smithwaterman/IndelAllele.cpp', | |
82 | + ] | |
83 | +endif | |
84 | ||
85 | ||
86 | # | |
99043adf | 87 | @@ -105,23 +160,18 @@ seqlib_src = [ |
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88 | ] |
89 | ||
90 | vcflib_src = [ | |
91 | - 'vcflib/tabixpp/tabix.cpp', | |
99043adf | 92 | - 'vcflib/src/Variant.cpp', |
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93 | - 'vcflib/smithwaterman/SmithWatermanGotoh.cpp', |
94 | - 'vcflib/smithwaterman/disorder.cpp', | |
95 | - 'vcflib/smithwaterman/Repeats.cpp', | |
96 | - 'vcflib/smithwaterman/LeftAlign.cpp', | |
97 | - 'vcflib/smithwaterman/IndelAllele.cpp', | |
99043adf | 98 | + vcflib_src, |
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99 | + tabixpp_src, |
100 | + smithwaterman_src, | |
101 | ] | |
102 | ||
103 | bamleftalign_src = [ | |
104 | 'src/bamleftalign.cpp', | |
105 | 'src/IndelAllele.cpp', | |
106 | 'contrib/SeqLib/src/BamWriter.cpp', | |
107 | - 'vcflib/fastahack/Fasta.cpp', | |
108 | - 'vcflib/smithwaterman/LeftAlign.cpp', | |
109 | - 'vcflib/smithwaterman/IndelAllele.cpp', | |
99043adf | 110 | - 'vcflib/src/split.cpp', |
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111 | + fastahack_src, |
112 | + smithwaterman_src, | |
99043adf | 113 | + vcflib_src, |
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114 | 'src/LeftAlign.cpp', |
115 | ] | |
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116 | |
117 | @@ -134,11 +184,9 @@ incdir = include_directories( | |
118 | 'ttmath', | |
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119 | 'contrib', |
120 | 'contrib/SeqLib', | |
99043adf | 121 | - 'vcflib/src', |
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122 | - 'vcflib/tabixpp', |
123 | - 'vcflib/smithwaterman', | |
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124 | - 'vcflib/multichoose', |
125 | - 'vcflib/filevercmp') | |
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126 | + tabixpp_includes, |
127 | + smithwaterman_includes, | |
99043adf | 128 | + vcflib_includes) |
fc9fd549 | 129 | |
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130 | c_args = ['-fpermissive','-w'] |
131 | cpp_args = ['-fpermissive','-w','-Wc++14-compat'] | |
132 | @@ -152,7 +200,7 @@ executable('freebayes', | |
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133 | include_directories : incdir, |
134 | cpp_args : cpp_args, | |
135 | c_args : c_args, | |
136 | - dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], | |
99043adf | 137 | + dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, smithwaterman_dep, vcflib_dep, thread_dep], |
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138 | install: true |
139 | ) | |
140 | ||
99043adf | 141 | @@ -165,7 +213,7 @@ executable('bamleftalign', |
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142 | include_directories : incdir, |
143 | cpp_args : cpp_args, | |
144 | c_args : c_args, | |
145 | - dependencies: [zlib_dep, lzma_dep, htslib_dep, thread_dep], | |
99043adf | 146 | + dependencies: [zlib_dep, lzma_dep, simde_dep, htslib_dep, tabixpp_dep, fastahack_dep, smithwaterman_dep, vcflib_dep, thread_dep], |
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147 | install: true |
148 | ) | |
149 | ||
150 | -- | |
151 | 2.30.0 | |
152 |