--- meson.build.orig	2025-02-16 14:02:36 UTC
+++ meson.build
@@ -15,7 +15,7 @@ project('freebayes', ['cpp', 'c'],
 
 project('freebayes', ['cpp', 'c'],
         version : '1.3.9',
-        default_options : ['warning_level=1', 'cpp_std=c++17', 'optimization=3'])
+        default_options : ['warning_level=1', 'cpp_std=c++14', 'optimization=3'])
 static_build = get_option('static')
 
 # used by Debian: add_global_arguments('-D_GLIBCXX_ASSERTIONS=1', language : 'cpp')
@@ -25,10 +25,12 @@ thread_dep = dependency('threads', static: static_buil
 # fastahack_dep = cc.find_library('libfastahack')
 lzma_dep = dependency('liblzma', static: static_build)
 thread_dep = dependency('threads', static: static_build)
-wfa2lib_dep = cc.find_library('libwfa2') # 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('libvcflib', required: false)
+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)
 
@@ -43,14 +45,12 @@ if get_option('prefer_system_deps') # defaults to true
 
 
 if get_option('prefer_system_deps') # defaults to true, otherwise use git modules and local sources
-  fastahack_dep = cc.find_library('libfastahack', required: true) # also link in for vcflib
-  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
+  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_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/
@@ -153,14 +153,14 @@ freebayes_lib = static_library(
     include_directories : [incdir, vcflib_inc, fastahack_inc],
     cpp_args : extra_cpp_args,
     dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
-                    vcflib_dep, wfa2lib_dep, seqlib_dep],
+                    vcflib_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',
@@ -177,6 +177,7 @@ executable('freebayes',
                           seqlib_dep,
                           fastahack_dep, # for vcflib
                           smithwaterman_dep, # for vcflib
+                          multichoose_dep,
                           wfa2lib_dep],
            link_with : freebayes_lib,
            install: true
@@ -195,6 +196,7 @@ executable('bamleftalign',
                           seqlib_dep,
                           fastahack_dep, # for vcflib
                           smithwaterman_dep, # for vcflib
+                          multichoose_dep,
                           wfa2lib_dep],
            link_with : freebayes_lib,
            install: true