gnu: freebayes: Update to 1.3.5.

* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.5.
[source]: Remove patch.
[arguments]: Adjust custom 'patch-source phase for changes in source.
[inputs]: Remove zlib.
* gnu/packages/patches/freebayes-devendor-deps.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.

3 files changed, 7 insertions, 162 deletions

diff --git a/gnu/local.mk b/gnu/local.mk
index 1c692e0ce4..153f6ee8d7 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1019,7 +1019,6 @@ dist_patch_DATA =						\
   %D%/packages/patches/fpc-reproducibility.patch		\
   %D%/packages/patches/fplll-std-fenv.patch     		\
   %D%/packages/patches/freedink-engine-fix-sdl-hints.patch	\
-  %D%/packages/patches/freebayes-devendor-deps.patch		\
   %D%/packages/patches/freeimage-unbundle.patch		\
   %D%/packages/patches/fuse-overlapping-headers.patch				\
   %D%/packages/patches/gajim-honour-GAJIM_PLUGIN_PATH.patch	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2de8a59d3c..1e38c6e0e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13572,7 +13572,7 @@ manipulations on VCF files.")
 (define-public freebayes
   (package
     (name "freebayes")
-    (version "1.3.3")
+    (version "1.3.5")
     (source (origin
               (method git-fetch)
               (uri (git-reference
@@ -13580,8 +13580,7 @@ manipulations on VCF files.")
                     (commit (string-append "v" version))))
               (file-name (git-file-name name version))
               (sha256
-               (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8"))
-              (patches (search-patches "freebayes-devendor-deps.patch"))
+               (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3"))
               (modules '((guix build utils)))
               (snippet
                '(begin
@@ -13593,8 +13592,7 @@ manipulations on VCF files.")
        ("htslib" ,htslib)
        ("smithwaterman" ,smithwaterman)
        ("tabixpp" ,tabixpp)
-       ("vcflib" ,vcflib)
-       ("zlib" ,zlib)))
+       ("vcflib" ,vcflib)))
     (native-inputs
      `(("bash-tap" ,bash-tap)
        ("bc" ,bc)
@@ -13627,13 +13625,13 @@ manipulations on VCF files.")
                   (string-append bash-tap "/bin/bash-tap-bootstrap"))
                  (("source.*bash-tap-bootstrap")
                   (string-append "source " bash-tap "/bin/bash-tap-bootstrap")))
-               (substitute* "meson.build"
-                  ;; Some inputs aren't actually needed.
-                 ((".*bamtools/src.*") "")
-                 ((".*multichoose.*") ""))
                (substitute* '("src/BedReader.cpp"
                               "src/BedReader.h")
                  (("../intervaltree/IntervalTree.h") "IntervalTree.h"))
+               (substitute* "meson.build"
+                 ;; Our pkg-config file is vcflib.pc
+                 (("libvcflib") "vcflib")
+                 (("vcflib_inc,") ""))
                #t)))
          (add-after 'unpack 'unpack-submodule-sources
            (lambda* (#:key inputs #:allow-other-keys)
diff --git a/gnu/packages/patches/freebayes-devendor-deps.patch b/gnu/packages/patches/freebayes-devendor-deps.patch
deleted file mode 100644
index 9886de11fb..0000000000
--- a/gnu/packages/patches/freebayes-devendor-deps.patch
+++ /dev/null
@@ -1,152 +0,0 @@
-This patch is original to Guix, ongoing work to upstream bits as possible.
-
-From 9acc56db5e7469f5976be38b52ba4993de98ee38 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 | 84 +++++++++++++++++++++++++++++++++++++++++------------
- 1 file changed, 66 insertions(+), 18 deletions(-)
-
-diff --git a/meson.build b/meson.build
-index f6bf242..bded4af 100644
---- a/meson.build
-+++ b/meson.build
-@@ -9,8 +9,13 @@ 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)
-+vcflib_dep = dependency('vcflib', required: false)
- thread_dep = dependency('threads')
- 
- if htslib_dep.found()
-@@ -59,6 +64,56 @@ else
- ]
- endif
- 
-+if tabixpp_dep.found()
-+  tabixpp_includes = ''
-+  tabixpp_src = []
-+else
-+  tabixpp_includes = [
-+    'vcflib/tabixpp',
-+    ]
-+  tabixpp_src = [
-+    'vcflib/tabixpp/tabix.cpp',
-+    ]
-+endif
-+
-+if vcflib_dep.found()
-+  vcflib_includes = ''
-+  vcflib_src = []
-+else
-+  vcflib_includes = [
-+    'vcflib/src',
-+    'vcflib/multichoose',
-+    'vcflib/filevercmp',
-+    ]
-+  vcflib_src = [
-+    'vcflib/src/Variant.cpp',
-+    ]
-+endif
-+
-+if fastahack_dep.found()
-+  fastahack_src = []
-+else
-+  fastahack_src = [
-+    'vcflib/fastahack/Fasta.cpp',
-+    'vcflib/src/split.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
- 
- 
- #
-@@ -105,23 +160,18 @@ 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',
-+    vcflib_src,
-+    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',
--    'vcflib/src/split.cpp',
-+    fastahack_src,
-+    smithwaterman_src,
-+    vcflib_src,
-     'src/LeftAlign.cpp',
- ]
- 
-@@ -134,11 +184,9 @@ incdir = include_directories(
-     'ttmath',
-     'contrib',
-     'contrib/SeqLib',
--    'vcflib/src',
--    'vcflib/tabixpp',
--    'vcflib/smithwaterman',
--    'vcflib/multichoose',
--    'vcflib/filevercmp')
-+    tabixpp_includes,
-+    smithwaterman_includes,
-+    vcflib_includes)
- 
- c_args = ['-fpermissive','-w']
- cpp_args = ['-fpermissive','-w','-Wc++14-compat']
-@@ -152,7 +200,7 @@ 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, vcflib_dep, thread_dep],
-            install: true
-           )
- 
-@@ -165,7 +213,7 @@ 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, vcflib_dep, thread_dep],
-            install: true
-           )
- 
--- 
-2.30.0
-