biology/vcflib: Update to 1.0.6

A few minor upstream fixes
Unbundle WFA2-lib, which may be useful outside vcflib
Update some submodules to latest commit (no recent releases available)

4 files changed, 28 insertions, 45 deletions

diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index 17002a8ccdbc..311b78bac7ce 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.0.5
-PORTREVISION=		2
+DISTVERSION=		1.0.6
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -13,25 +12,26 @@ LICENSE=	MIT
 BUILD_DEPENDS=	zig>0:lang/zig \
 		pybind11>=0:devel/pybind11
 LIB_DEPENDS=	libhts.so:biology/htslib \
-		libcurl.so:ftp/curl
+		libcurl.so:ftp/curl \
+		libwfa2.so:biology/wfa2-lib
 
 USES=		cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	ekg
 GH_TUPLE=	ekg:fastahack:bb33265:fastahack/contrib/fastahack \
-		ekg:filevercmp:1a9b779:filevercmp/contrib/filevercmp \
-		ekg:fsom:a6ef318:fsom/contrib/fsom \
-		google:googletest:d225acc:googletest/contrib/googletest \
+		ekg:filevercmp:df20dcc:filevercmp/contrib/filevercmp \
+		ekg:fsom:56695e1:fsom/contrib/fsom \
 		ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \
 		edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \
-		ekg:multichoose:68733cd:multichoose/contrib/multichoose \
+		ekg:multichoose:e1f94ae:multichoose/contrib/multichoose \
 		ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \
 		simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \
-		vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp \
-		smarco:WFA2-lib:v2.3:wfa2/contrib/WFA2-lib
+		vcflib:tabixpp:v1.1.2:tabixpp/contrib/tabixpp
 SHEBANG_FILES=	scripts/*
 
+CMAKE_ARGS+=	-DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so
+
 # Clang and GCC disable sse2 by default on i386, but it's required for vcflib
 CFLAGS_i386=	-msse2
 
diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo
index b009e8c070e7..b31324e88085 100644
--- a/biology/vcflib/distinfo
+++ b/biology/vcflib/distinfo
@@ -1,25 +1,21 @@
-TIMESTAMP = 1674400989
-SHA256 (ekg-vcflib-v1.0.5_GH0.tar.gz) = f24b8553fcb37dfe35e704a415ff4be8fd657a5d94f0101723552805946fb7a3
-SIZE (ekg-vcflib-v1.0.5_GH0.tar.gz) = 23545058
+TIMESTAMP = 1675089755
+SHA256 (ekg-vcflib-v1.0.6_GH0.tar.gz) = 3598d1a9f6c936c58be6a567f249c1df879a49b57dc5a967b83a7856a16ceeb6
+SIZE (ekg-vcflib-v1.0.6_GH0.tar.gz) = 23545077
 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
 SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
-SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
-SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
-SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
-SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
-SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
-SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
+SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059
+SIZE (ekg-filevercmp-df20dcc_GH0.tar.gz) = 3113
+SHA256 (ekg-fsom-56695e1_GH0.tar.gz) = d1cc62bf72a75b74149336799fcbe237eaa662161fb0cfdac5ba6d5825248180
+SIZE (ekg-fsom-56695e1_GH0.tar.gz) = 9767
 SHA256 (ekg-intervaltree-aa59377_GH0.tar.gz) = 8d42eee645bcb196da03077c6f567f61529add3a581bb98d85f5c9cfe4b50774
 SIZE (ekg-intervaltree-aa59377_GH0.tar.gz) = 72545
 SHA256 (edawson-libVCFH-44b6580_GH0.tar.gz) = 3c90a6c5f1fbe88bedb4a0dcdc1e55dfa51c58f2acd9b31bceead226ab84785c
 SIZE (edawson-libVCFH-44b6580_GH0.tar.gz) = 2956
-SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
-SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
+SHA256 (ekg-multichoose-e1f94ae_GH0.tar.gz) = 78ffaa36b6f82685230a3d263c9b556ab55a97196036764473f2b1ee66997ca8
+SIZE (ekg-multichoose-e1f94ae_GH0.tar.gz) = 6585
 SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
 SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
 SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe
 SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867
 SHA256 (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc
 SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962
-SHA256 (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 64a113895c74dd746ec52d768a2d56465fb4a86c40c13fe985af549f1ca86343
-SIZE (smarco-WFA2-lib-v2.3_GH0.tar.gz) = 4149234
diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt
index 6de651bd1d98..5a7824a2dfa0 100644
--- a/biology/vcflib/files/patch-CMakeLists.txt
+++ b/biology/vcflib/files/patch-CMakeLists.txt
@@ -1,6 +1,6 @@
---- CMakeLists.txt.orig	2023-01-16 08:55:05 UTC
+--- CMakeLists.txt.orig	2023-01-29 04:57:02 UTC
 +++ CMakeLists.txt
-@@ -1,7 +1,7 @@
+@@ -9,7 +9,7 @@
  cmake_minimum_required(VERSION 3.16)
  project(vcflib)
  
@@ -9,15 +9,12 @@
  
  include(ExternalProject)
  include(FeatureSummary)
-@@ -358,9 +358,9 @@ endif(HTSLIB_LOCAL)
+@@ -38,7 +38,7 @@ option(PROFILING "Enable profiling" OFF)
+ option(GPROF "Enable gprof profiling" OFF)
+ option(ASAN "Use address sanitiser" OFF)
+ option(ZIG "Set to OFF to disable the zig code" ON)
+-option(WFA_GITMODULE "Force local git submodule for WFA2LIB" ON) # disable in distros, you may need to add path to WFA_INCLUDE_DIRS
++option(WFA_GITMODULE "Force local git submodule for WFA2LIB" OFF) # disable in distros, you may need to add path to WFA_INCLUDE_DIRS
  
- # FIXME: hard-coded compile switches need to be fixed upstream
- if (ASAN)
--  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup asan lib_wfa)
-+  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup asan lib_wfa)
- else()
--  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup lib_wfa)
-+  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa)
- endif()
- 
- # if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo))
+ include(CheckIPOSupported) # adds lto
+ check_ipo_supported(RESULT ipo_supported OUTPUT output)
diff --git a/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h b/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h
deleted file mode 100644
index c954e2132183..000000000000
--- a/biology/vcflib/files/patch-contrib_WFA2-lib_system_profiler__timer.h
+++ /dev/null
@@ -1,10 +0,0 @@
---- contrib/WFA2-lib/system/profiler_timer.h.orig	2023-01-26 13:43:09 UTC
-+++ contrib/WFA2-lib/system/profiler_timer.h
-@@ -33,6 +33,7 @@
- #ifndef PROFILER_TIMER_H
- #define PROFILER_TIMER_H
- 
-+#include <time.h>
- #include "profiler_counter.h"
- 
- /*