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bac90e855c
Upstream moved away from git submodules to external deps Several fixes since 1.3.6 Changes: https://github.com/freebayes/freebayes/releases Reported by: portscout
81 lines
3.7 KiB
Text
81 lines
3.7 KiB
Text
--- meson.build.orig 2025-02-16 14:02:36 UTC
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+++ meson.build
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@@ -15,7 +15,7 @@ project('freebayes', ['cpp', 'c'],
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project('freebayes', ['cpp', 'c'],
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version : '1.3.9',
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- default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
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+ default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3'])
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static_build = get_option('static')
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# used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp')
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@@ -25,10 +25,12 @@ thread_dep = dependency('threads', static: static_buil
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# fastahack_dep = cc.find_library('libfastahack')
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lzma_dep = dependency('liblzma', static: static_build)
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thread_dep = dependency('threads', static: static_build)
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-wfa2lib_dep = cc.find_library('libwfa2') # need to link for vcflib code
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+wfa2_inc = include_directories('/usr/local/include/wfa2lib')
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+wfa2lib_dep = declare_dependency(include_directories: wfa2_inc)
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zlib_dep = dependency('zlib', static: static_build)
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htslib_dep = dependency('htslib', static: static_build, required: false)
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-vcflib_dep = cc.find_library('libvcflib', required: false)
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+vcflib_inc = include_directories('/usr/local/include/vcflib')
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+vcflib_dep = declare_dependency(link_args: '-lvcflib', include_directories: vcflib_inc)
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seqlib_dep = dependency('libseqlib', static: static_build, required: false)
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tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
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@@ -43,14 +45,12 @@ if get_option('prefer_system_deps') # defaults to true
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if get_option('prefer_system_deps') # defaults to true, otherwise use git modules and local sources
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- fastahack_dep = cc.find_library('libfastahack', required: true) # also link in for vcflib
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- smithwaterman_dep = cc.find_library('libsmithwaterman')
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- if fs.is_dir('/usr/include/fastahack')
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- message('Using /usr/include/fastahack dir')
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- fastahack_inc = include_directories('/usr/include/fastahack')
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- else
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- fastahack_inc = files()
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- endif
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+ fastahack_inc = include_directories('/usr/local/include/fastahack')
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+ fastahack_dep = declare_dependency(include_directories: fastahack_inc)
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+ sw_inc = include_directories('/usr/local/include/smithwaterman')
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+ smithwaterman_dep = declare_dependency(include_directories: sw_inc)
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+ multichoose_inc = include_directories('/usr/local/include/multichoose')
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+ multichoose_dep = declare_dependency(include_directories: multichoose_inc)
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else
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# uses the minimal local git submodules or checkout trees in ./contrib/
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@@ -153,14 +153,14 @@ freebayes_lib = static_library(
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include_directories : [incdir, vcflib_inc, fastahack_inc],
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cpp_args : extra_cpp_args,
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dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
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- vcflib_dep, wfa2lib_dep, seqlib_dep],
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+ vcflib_dep, wfa2lib_dep, seqlib_dep, multichoose_dep],
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install : false,
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)
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if static_build
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- link_arguments = '-static'
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+ link_arguments = '-static -L/usr/local/lib'
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else
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- link_arguments = []
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+ link_arguments = '-L/usr/local/lib'
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endif
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executable('freebayes',
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@@ -177,6 +177,7 @@ executable('freebayes',
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seqlib_dep,
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fastahack_dep, # for vcflib
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smithwaterman_dep, # for vcflib
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+ multichoose_dep,
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wfa2lib_dep],
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link_with : freebayes_lib,
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install: true
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@@ -195,6 +196,7 @@ executable('bamleftalign',
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seqlib_dep,
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fastahack_dep, # for vcflib
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smithwaterman_dep, # for vcflib
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+ multichoose_dep,
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wfa2lib_dep],
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link_with : freebayes_lib,
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install: true
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