From b65c02e2d35af6fbe1d1810d6c69cfab194e13e2 Mon Sep 17 00:00:00 2001
From: Efraim Flashner <efraim@flashner.co.il>
Date: Sun, 6 Jun 2021 12:07:01 +0300
Subject: 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.
---
 gnu/packages/patches/freebayes-devendor-deps.patch | 152 ---------------------
 1 file changed, 152 deletions(-)
 delete mode 100644 gnu/packages/patches/freebayes-devendor-deps.patch

(limited to 'gnu/packages/patches/freebayes-devendor-deps.patch')

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
-
-- 
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