git: 459cb897f042 - main - biology/vcflib: Update to 1.0.5

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Sun, 22 Jan 2023 17:14:40 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=459cb897f0423111cd4b55fac5caabeef7c81d77

commit 459cb897f0423111cd4b55fac5caabeef7c81d77
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2023-01-22 17:13:14 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2023-01-22 17:13:14 +0000

    biology/vcflib: Update to 1.0.5
    
    Numerous new features and enhancements
    
    Changes:    https://github.com/vcflib/vcflib/tags
    
    Reported by:    portscout
---
 biology/vcflib/Makefile                   | 32 ++++++++++++++++++-------------
 biology/vcflib/distinfo                   | 10 +++++++---
 biology/vcflib/files/patch-CMakeLists.txt | 30 ++++++++++++++++++++---------
 biology/vcflib/pkg-plist                  | 14 ++++++++++++++
 4 files changed, 61 insertions(+), 25 deletions(-)

diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index a42fa6c8898e..7038f110c052 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -1,7 +1,6 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.0.3
-PORTREVISION=		1
+DISTVERSION=		1.0.5
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -10,22 +9,26 @@ WWW=		https://github.com/vcflib/vcflib
 
 LICENSE=	MIT
 
+BUILD_DEPENDS=	zig>0:lang/zig \
+		pybind11>=0:devel/pybind11
 LIB_DEPENDS=	libhts.so:biology/htslib \
-		libtabix.so:biology/tabixpp
+		libcurl.so:ftp/curl
 
-USES=		cmake localbase:ldflags pkgconfig python shebangfix
+USES=		cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix
 USE_GITHUB=	yes
 
 GH_ACCOUNT=	ekg
-GH_TUPLE=	ekg:fastahack:bb33265:fastahack/fastahack \
-		ekg:filevercmp:1a9b779:filevercmp/filevercmp \
-		ekg:fsom:a6ef318:fsom/fsom \
-		google:googletest:d225acc:googletest/googletest \
-		ekg:intervaltree:aa59377:intervaltree/intervaltree \
-		edawson:libVCFH:44b6580:libVCFH/libVCFH \
-		ekg:multichoose:68733cd:multichoose/multichoose \
-		ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \
-		simd-everywhere:simde-no-tests:9af03cd:simd/src/simde
+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:intervaltree:aa59377:intervaltree/contrib/intervaltree \
+		edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \
+		ekg:multichoose:68733cd: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
 SHEBANG_FILES=	scripts/*
 
 # Clang and GCC disable sse2 by default on i386, but it's required for vcflib
@@ -33,4 +36,7 @@ CFLAGS_i386=	-msse2
 
 CONFLICTS_INSTALL=	filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp
 
+post-stage:
+	${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib
+
 .include <bsd.port.mk>
diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo
index bdbfdb931717..b009e8c070e7 100644
--- a/biology/vcflib/distinfo
+++ b/biology/vcflib/distinfo
@@ -1,6 +1,6 @@
-TIMESTAMP = 1643316477
-SHA256 (ekg-vcflib-v1.0.3_GH0.tar.gz) = 5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c
-SIZE (ekg-vcflib-v1.0.3_GH0.tar.gz) = 19213097
+TIMESTAMP = 1674400989
+SHA256 (ekg-vcflib-v1.0.5_GH0.tar.gz) = f24b8553fcb37dfe35e704a415ff4be8fd657a5d94f0101723552805946fb7a3
+SIZE (ekg-vcflib-v1.0.5_GH0.tar.gz) = 23545058
 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
 SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
 SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
@@ -19,3 +19,7 @@ SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905
 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 2520c928273e..6de651bd1d98 100644
--- a/biology/vcflib/files/patch-CMakeLists.txt
+++ b/biology/vcflib/files/patch-CMakeLists.txt
@@ -1,11 +1,23 @@
---- CMakeLists.txt.orig	2021-11-03 15:07:33 UTC
+--- CMakeLists.txt.orig	2023-01-16 08:55:05 UTC
 +++ CMakeLists.txt
-@@ -230,7 +230,7 @@ if (NOT BUILD_ONLY_LIB)
-   foreach(BIN ${BINS})
-     add_executable(${BIN} src/${BIN}.cpp)
-     target_include_directories(${BIN} PUBLIC ${TABIXPP_LIBRARIES} ${HTSLIB_INCLUDE_DIRS})
--    target_link_libraries(${BIN} vcflib tabixpp -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES})
-+    target_link_libraries(${BIN} vcflib tabix -DGIT_VERSION=0.9.0 ${TABIXPP_LIBRARIES} ${HTSLIB_LIBRARIES} ${CMAKE_THREAD_LIBS_INIT} ${ZLIB_LIBRARIES} ${LIBLZMA_LIBRARIES} ${BZIP2_LIBRARIES})
-   endforeach(BIN ${BINS})
-   install(TARGETS ${BINS} RUNTIME DESTINATION bin)
+@@ -1,7 +1,7 @@
+ cmake_minimum_required(VERSION 3.16)
+ project(vcflib)
+ 
+-set(CMAKE_CXX_STANDARD 17)
++set(CMAKE_CXX_STANDARD 14)
+ 
+ include(ExternalProject)
+ include(FeatureSummary)
+@@ -358,9 +358,9 @@ endif(HTSLIB_LOCAL)
+ 
+ # FIXME: hard-coded compile switches need to be fixed upstream
+ if (ASAN)
+-  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup asan lib_wfa)
++  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup asan lib_wfa)
+ else()
+-  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC=gcc CC_FLAGS=-fPIC setup lib_wfa)
++  set(wfa_MAKE_ARGS BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa)
  endif()
+ 
+ # if ((${CMAKE_BUILD_TYPE} MATCHES Release) OR (${CMAKE_BUILD_TYPE} MATCHES RelWithDebInfo))
diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist
index 14fd56d8448f..b5b53667909c 100644
--- a/biology/vcflib/pkg-plist
+++ b/biology/vcflib/pkg-plist
@@ -82,6 +82,7 @@ bin/vcfnobiallelicsnps
 bin/vcfnoindels
 bin/vcfnosnps
 bin/vcfnulldotslashdot
+bin/vcfnullgenofields
 bin/vcfnumalt
 bin/vcfoverlay
 bin/vcfparsealts
@@ -116,6 +117,7 @@ bin/vcfstreamsort
 bin/vcfuniq
 bin/vcfuniqalleles
 bin/vcfvarstats
+bin/vcfwave
 bin/wcFst
 include/BandedSmithWaterman.h
 include/BedReader.h
@@ -124,13 +126,16 @@ include/IndelAllele.h
 include/IntervalTree.h
 include/LargeFileSupport.h
 include/LeftAlign.h
+include/LeftAlign.hpp
 include/Mosaik.h
 include/Region.h
 include/Repeats.h
 include/SmithWatermanGotoh.h
 include/Variant.h
+include/allele.hpp
 include/catch.hpp
 include/cdflib.hpp
+include/cigar.hpp
 include/convert.h
 include/disorder.h
 include/filevercmp.h
@@ -140,15 +145,20 @@ include/makeUnique.h
 include/mt19937ar.h
 include/multichoose.h
 include/multipermute.h
+include/murmur3.hpp
 include/pdflib.hpp
+include/rkmh.hpp
 include/rnglib.hpp
 include/split.h
 include/ssw.hpp
 include/ssw_cpp.hpp
 include/var.hpp
+include/vcf-c-api.h
 include/vec128int.h
 include/veclib_types.h
 lib/libvcflib.a
+lib/libzig.a
+lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
 man/man1/abba-baba.1.gz
 man/man1/bFst.1.gz
 man/man1/dumpContigsFromHeader.1.gz
@@ -163,6 +173,7 @@ man/man1/permuteGPAT++.1.gz
 man/man1/permuteSmooth.1.gz
 man/man1/plotHaps.1.gz
 man/man1/popStats.1.gz
+man/man1/pyvcflib.1.gz
 man/man1/segmentFst.1.gz
 man/man1/segmentIhs.1.gz
 man/man1/sequenceDiversity.1.gz
@@ -212,8 +223,10 @@ man/man1/vcfkeepsamples.1.gz
 man/man1/vcfld.1.gz
 man/man1/vcfleftalign.1.gz
 man/man1/vcflength.1.gz
+man/man1/vcflib-api.1.gz
 man/man1/vcflib.1.gz
 man/man1/vcfnulldotslashdot.1.gz
+man/man1/vcfnullgenofields.1.gz
 man/man1/vcfnumalt.1.gz
 man/man1/vcfoverlay.1.gz
 man/man1/vcfparsealts.1.gz
@@ -233,4 +246,5 @@ man/man1/vcfstats.1.gz
 man/man1/vcfstreamsort.1.gz
 man/man1/vcfuniq.1.gz
 man/man1/vcfuniqalleles.1.gz
+man/man1/vcfwave.1.gz
 man/man1/wcFst.1.gz