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