--- meson.build.orig	2025-05-31 07:44:14 UTC
+++ meson.build
@@ -22,7 +22,6 @@ project('freebayes', ['cpp', 'c'],
 project('freebayes', ['cpp', 'c'],
         version : '1.3.10',
         default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
-add_global_arguments('-Wno-maybe-uninitialized', language : 'cpp') # for ttmath warnings
 
 static_build = get_option('static')
 
@@ -32,12 +31,16 @@ thread_dep = dependency('threads', static: static_buil
 
 lzma_dep = dependency('liblzma', static: static_build)
 thread_dep = dependency('threads', static: static_build)
-wfa2lib_dep = cc.find_library('wfa2') # need to link for vcflib code
+wfa2_inc = include_directories('/usr/local/include/wfa2lib')
+wfa2lib_dep = declare_dependency(include_directories: wfa2_inc)
 zlib_dep = dependency('zlib', static: static_build)
 htslib_dep = dependency('htslib', static: static_build, required: false)
-vcflib_dep = cc.find_library('vcflib', required: false, static: static_build)
+vcflib_inc = include_directories('/usr/local/include/vcflib')
+vcflib_dep = declare_dependency(link_args: '-lvcflib', include_directories: vcflib_inc)
 seqlib_dep = dependency('libseqlib', static: static_build, required: false)
 tabixpp_dep = cc.find_library('tabixpp', required: false, static: static_build)
+tabixpp_inc = include_directories('/usr/local/include')
+tabixpp_dep = declare_dependency(link_args: '-ltabix', include_directories: tabixpp_inc)
 
 # later versions of vcflib have Variant.hpp in a system subdirectory
 fs = import('fs')
@@ -49,19 +52,13 @@ if get_option('prefer_system_deps')
 endif
 
 if get_option('prefer_system_deps')
-  fastahack_dep = cc.find_library('libfastahack', required: true) # also link in for vcflib
-  fastahack_src = files()
-  smithwaterman_dep = cc.find_library('libsmithwaterman')
-  if fs.is_dir('/usr/include/fastahack')
-    message('Using /usr/include/fastahack dir')
-    fastahack_inc = include_directories('/usr/include/fastahack')
-  else
-    fastahack_inc = files()
-  endif
-  vcflib_inc = files()
-  vcflib_src = files()
-  smithwaterman_inc = files()
-  smithwaterman_src = files()
+  fastahack_inc = include_directories('/usr/local/include/fastahack')
+  fastahack_dep = declare_dependency(include_directories: fastahack_inc)
+  sw_inc = include_directories('/usr/local/include/smithwaterman')
+  smithwaterman_inc = include_directories('/usr/local/include/smithwaterman')
+  smithwaterman_dep = declare_dependency(include_directories: sw_inc)
+  multichoose_inc = include_directories('/usr/local/include/multichoose')
+  multichoose_dep = declare_dependency(include_directories: multichoose_inc)
 else
   # uses the minimal local git submodules or checkout trees in ./contrib/
   # see `git submodule`
@@ -153,8 +150,8 @@ bamleftalign_src = files('src/bamleftalign.cpp')
 freebayes_src = files('src/freebayes.cpp')
 bamleftalign_src = files('src/bamleftalign.cpp')
 
-freebayes_common_src += vcflib_src
-freebayes_common_src += smithwaterman_src
+# freebayes_common_src += vcflib_src
+# freebayes_common_src += smithwaterman_src
 
 # Include paths
 incdir = include_directories(
@@ -172,19 +169,19 @@ freebayes_lib = static_library(
 
 freebayes_lib = static_library(
     'freebayes_common',
-    [freebayes_common_src, fastahack_src],
+    [freebayes_common_src],
     pic: false,
     include_directories : [incdir, vcflib_inc, smithwaterman_inc, fastahack_inc],
     cpp_args : extra_cpp_args,
     dependencies : [vcflib_dep, zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
-                    wfa2lib_dep, seqlib_dep],
+                    wfa2lib_dep, seqlib_dep, multichoose_dep],
     install : false,
     )
 
 if static_build
-  link_arguments = '-static'
+  link_arguments = '-static -L/usr/local/lib'
 else
-  link_arguments = []
+  link_arguments = '-L/usr/local/lib'
 endif
 
 executable('freebayes',
@@ -201,7 +198,8 @@ executable('freebayes',
                           tabixpp_dep,
                           seqlib_dep,
                           fastahack_dep, # for vcflib
-                          smithwaterman_dep # for vcflib
+                          smithwaterman_dep, # for vcflib
+			  multichoose_dep
                           ],
            link_with : [freebayes_lib],
            install: true
@@ -220,7 +218,8 @@ executable('bamleftalign',
                           seqlib_dep,
                           fastahack_dep, # for vcflib
                           smithwaterman_dep, # for vcflib
-                          wfa2lib_dep],
+                          wfa2lib_dep,
+			  multichoose_dep],
            link_with : freebayes_lib,
            install: true
           )