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