git: 92b409e96b14 - main - biology/freebayes: Update to 1.3.10
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Date: Tue, 01 Sep 2026 21:36:50 UTC
The branch main has been updated by jwb:
URL: https://cgit.FreeBSD.org/ports/commit/?id=92b409e96b143e14637cb48d824a5c1c8cdfa798
commit 92b409e96b143e14637cb48d824a5c1c8cdfa798
Author: Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-01 21:36:13 +0000
Commit: Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-01 21:36:13 +0000
biology/freebayes: Update to 1.3.10
A few fixes and enhancements
Changes: https://github.com/freebayes/freebayes/releases
Reported by: portscout
---
biology/freebayes/Makefile | 2 +-
biology/freebayes/distinfo | 6 +-
...ntrib_SeqLib_SeqLib_GenomicRegionCollection.cpp | 21 ++++++
biology/freebayes/files/patch-meson.build | 86 +++++++++++++++-------
4 files changed, 83 insertions(+), 32 deletions(-)
diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile
index 3490bfcab6b7..90382bac8968 100644
--- a/biology/freebayes/Makefile
+++ b/biology/freebayes/Makefile
@@ -1,6 +1,6 @@
PORTNAME= freebayes
DISTVERSIONPREFIX= v
-DISTVERSION= 1.3.9
+DISTVERSION= 1.3.10
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
diff --git a/biology/freebayes/distinfo b/biology/freebayes/distinfo
index bc28d91cd6b1..e3c377f800ce 100644
--- a/biology/freebayes/distinfo
+++ b/biology/freebayes/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1739833701
-SHA256 (ekg-freebayes-v1.3.9_GH0.tar.gz) = 41ed3074c7648375286168a6708e02dac6788eaca4ca6039ff5a7ed91f257b53
-SIZE (ekg-freebayes-v1.3.9_GH0.tar.gz) = 2896143
+TIMESTAMP = 1788297685
+SHA256 (ekg-freebayes-v1.3.10_GH0.tar.gz) = 31900e4ad23f471310838f0ae6f6020b159bf5fa3d9826de285c4c91bfe0eeb2
+SIZE (ekg-freebayes-v1.3.10_GH0.tar.gz) = 2937728
diff --git a/biology/freebayes/files/patch-contrib_SeqLib_SeqLib_GenomicRegionCollection.cpp b/biology/freebayes/files/patch-contrib_SeqLib_SeqLib_GenomicRegionCollection.cpp
new file mode 100644
index 000000000000..ed2d1c12a370
--- /dev/null
+++ b/biology/freebayes/files/patch-contrib_SeqLib_SeqLib_GenomicRegionCollection.cpp
@@ -0,0 +1,21 @@
+--- contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp.orig 2026-09-01 21:13:10 UTC
++++ contrib/SeqLib/SeqLib/GenomicRegionCollection.cpp
+@@ -8,6 +8,7 @@
+ #include <stdexcept>
+ #include <algorithm>
+ #include <zlib.h>
++#include <random>
+
+ #define GZBUFFER 65472
+
+@@ -75,7 +76,9 @@ namespace SeqLib {
+
+ template<class T>
+ void GenomicRegionCollection<T>::Shuffle() {
+- std::random_shuffle ( m_grv->begin(), m_grv->end() );
++ std::random_device rd;
++ std::mt19937 g(rd());
++ std::shuffle ( m_grv->begin(), m_grv->end(), g );
+ }
+
+ template<class T>
diff --git a/biology/freebayes/files/patch-meson.build b/biology/freebayes/files/patch-meson.build
index c206bd537c7e..ae7648076ebf 100644
--- a/biology/freebayes/files/patch-meson.build
+++ b/biology/freebayes/files/patch-meson.build
@@ -1,34 +1,38 @@
---- meson.build.orig 2025-02-16 14:02:36 UTC
+--- meson.build.orig 2025-05-31 07:44:14 UTC
+++ meson.build
-@@ -15,7 +15,7 @@ project('freebayes', ['cpp', 'c'],
-
+@@ -22,7 +22,6 @@ 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'])
+ 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')
- # 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')
+@@ -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('libwfa2') # need to link for vcflib code
+-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('libvcflib', 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)
-@@ -43,14 +45,12 @@ if get_option('prefer_system_deps') # defaults to true
-
+ # 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') # defaults to true, otherwise use git modules and local sources
+ 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')
@@ -36,21 +40,43 @@
- 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/
-@@ -153,14 +153,14 @@ freebayes_lib = static_library(
- include_directories : [incdir, vcflib_inc, fastahack_inc],
+ # 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 : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep,
-- vcflib_dep, wfa2lib_dep, seqlib_dep],
-+ vcflib_dep, wfa2lib_dep, seqlib_dep, multichoose_dep],
+ 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,
)
@@ -63,19 +89,23 @@
endif
executable('freebayes',
-@@ -177,6 +177,7 @@ executable('freebayes',
+@@ -201,7 +198,8 @@ executable('freebayes',
+ tabixpp_dep,
seqlib_dep,
fastahack_dep, # for vcflib
- smithwaterman_dep, # for vcflib
-+ multichoose_dep,
- wfa2lib_dep],
- link_with : freebayes_lib,
+- smithwaterman_dep # for vcflib
++ smithwaterman_dep, # for vcflib
++ multichoose_dep
+ ],
+ link_with : [freebayes_lib],
install: true
-@@ -195,6 +196,7 @@ executable('bamleftalign',
+@@ -220,7 +218,8 @@ executable('bamleftalign',
seqlib_dep,
fastahack_dep, # for vcflib
smithwaterman_dep, # for vcflib
-+ multichoose_dep,
- wfa2lib_dep],
+- wfa2lib_dep],
++ wfa2lib_dep,
++ multichoose_dep],
link_with : freebayes_lib,
install: true
+ )