biology/vcflib: Update to 1.0.12

A few fixes and enhancements
Changes: https://github.com/vcflib/vcflib/releases

Reported by:    portscout

biology/vcflib/Makefile

@@ -1,6 +1,6 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.0.10
+DISTVERSION=		1.0.12
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -12,7 +12,8 @@ LICENSE=	MIT
 NOT_FOR_ARCHS=	armv6 armv7
 NOT_FOR_ARCHS_REASON=	requires OpenMP which is not supported
 
-BUILD_DEPENDS=	pybind11>0:devel/pybind11
+BUILD_DEPENDS=	pybind11>0:devel/pybind11 \
+		${PYTHON_PKGNAMEPREFIX}pypandoc>=1.4:textproc/py-pypandoc@${PY_FLAVOR}
 LIB_DEPENDS=	libhts.so:biology/htslib \
 		libcurl.so:ftp/curl \
 		libwfa2.so:biology/wfa2-lib
@@ -29,7 +30,7 @@ GH_TUPLE=	ekg:fastahack:bb33265:fastahack/contrib/fastahack \
 		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
+		vcflib:tabixpp:ae5cdf8:tabixpp/contrib/tabixpp
 SHEBANG_FILES=	scripts/*
 
 # FIXME: Add Zig option + lang/zig dep
@@ -39,10 +40,9 @@ OPTIONS_SUB=		yes
 
 ZIG_DESC=		Include Zig language support
 
-# FIXME: https://github.com/vcflib/vcflib/issues/399
+ZIG_BUILD_DEPENDS=	zig>0:lang/zig
-ZIG_BUILD_DEPENDS=	zig010>0:lang/zig010
 
-CMAKE_ARGS+=	-DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so
+CMAKE_ARGS+=	-DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0
 ZIG_CMAKE_OFF=	-DZIG=OFF
 
 # Clang and GCC disable sse2 by default on i386, but it's required for vcflib

biology/vcflib/distinfo

@@ -1,6 +1,6 @@
-TIMESTAMP = 1713703391
+TIMESTAMP = 1732541764
-SHA256 (ekg-vcflib-v1.0.10_GH0.tar.gz) = 6f7f366555e5b191a509bda6d7a2078825827458ba7e9922094c4c1ebb48e693
+SHA256 (ekg-vcflib-v1.0.12_GH0.tar.gz) = 7ab5b6a87a39105107029f5e0da52ece612c71095ab2aec69a00320f44bc5300
-SIZE (ekg-vcflib-v1.0.10_GH0.tar.gz) = 23539349
+SIZE (ekg-vcflib-v1.0.12_GH0.tar.gz) = 23543176
 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
 SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
 SHA256 (ekg-filevercmp-df20dcc_GH0.tar.gz) = d34bec614be638e05eb6fa419c936b9e7de58d50b1a096a5ca02aadb7db6b059
@@ -17,5 +17,5 @@ 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
+SHA256 (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = edb15012b57c6bfc900c1b8275fc3d55f2e7c21e83601f8cfedcbdf3107fbb04
-SIZE (vcflib-tabixpp-v1.1.2_GH0.tar.gz) = 6962
+SIZE (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = 6965

biology/vcflib/files/patch-CMakeLists.txt

@@ -1,15 +1,6 @@
---- CMakeLists.txt.orig	2023-02-07 17:22:46 UTC
+--- CMakeLists.txt.orig	2024-11-21 07:59:50 UTC
 +++ CMakeLists.txt
-@@ -9,7 +9,7 @@ project(vcflib)
+@@ -70,7 +70,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
- cmake_minimum_required(VERSION 3.16)
- project(vcflib)
- 
--set(CMAKE_CXX_STANDARD 17)
-+set(CMAKE_CXX_STANDARD 14)
- 
- include(ExternalProject)
- include(FeatureSummary)
-@@ -69,7 +69,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release)
  endif()
  
  if (${CMAKE_BUILD_TYPE} MATCHES Release)
@@ -18,9 +9,14 @@
    # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast
  endif()
  
-@@ -570,4 +570,4 @@ install(FILES ${INCLUDES} DESTINATION include)
+@@ -595,8 +595,8 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS
+ # ---- Install
  
- install(FILES ${INCLUDES} DESTINATION include)
+ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
+-install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
++# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR})
+ 
+ install(FILES ${INCLUDES} DESTINATION include/vcflib)
  
 -install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/man/man1)
 +install(DIRECTORY ${CMAKE_SOURCE_DIR}/man/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/man/man1)

biology/vcflib/pkg-plist

@@ -26,7 +26,6 @@ bin/vcf2tsv
 bin/vcf_strip_extra_headers
 bin/vcfaddinfo
 bin/vcfafpath
-bin/vcfallelicprimitives
 bin/vcfaltcount
 bin/vcfannotate
 bin/vcfannotategenotypes
@@ -35,7 +34,6 @@ bin/vcfbreakmulti
 bin/vcfcat
 bin/vcfcheck
 bin/vcfclassify
-bin/vcfcleancomplex
 bin/vcfclearid
 bin/vcfclearinfo
 bin/vcfcombine
@@ -85,7 +83,6 @@ bin/vcfnulldotslashdot
 bin/vcfnullgenofields
 bin/vcfnumalt
 bin/vcfoverlay
-bin/vcfparsealts
 bin/vcfplotaltdiscrepancy.r
 bin/vcfplotaltdiscrepancy.sh
 bin/vcfplotsitediscrepancy.r
@@ -105,59 +102,57 @@ bin/vcfremap
 bin/vcfremoveaberrantgenotypes
 bin/vcfremovenonATGC
 bin/vcfremovesamples
-bin/vcfroc
 bin/vcfsample2info
 bin/vcfsamplediff
 bin/vcfsamplenames
 bin/vcfsitesummarize
 bin/vcfsnps
 bin/vcfsort
-bin/vcfstats
 bin/vcfstreamsort
 bin/vcfuniq
 bin/vcfuniqalleles
 bin/vcfvarstats
-bin/vcfwave
 bin/wcFst
-include/BandedSmithWaterman.h
+include/vcflib/BandedSmithWaterman.h
-include/BedReader.h
+include/vcflib/BedReader.h
-include/Fasta.h
+include/vcflib/Fasta.h
-include/IndelAllele.h
+include/vcflib/IndelAllele.h
-include/IntervalTree.h
+include/vcflib/IntervalTree.h
-include/LargeFileSupport.h
+include/vcflib/LargeFileSupport.h
-include/LeftAlign.h
+include/vcflib/LeftAlign.h
-include/LeftAlign.hpp
+include/vcflib/LeftAlign.hpp
-include/Mosaik.h
+include/vcflib/Mosaik.h
-include/Region.h
+include/vcflib/Region.h
-include/Repeats.h
+include/vcflib/Repeats.h
-include/SmithWatermanGotoh.h
+include/vcflib/SmithWatermanGotoh.h
-include/Variant.h
+include/vcflib/Variant.h
-include/allele.hpp
+include/vcflib/allele.hpp
-include/catch.hpp
+include/vcflib/canonicalize.h
-include/cdflib.hpp
+include/vcflib/catch.hpp
-include/cigar.hpp
+include/vcflib/cdflib.hpp
-include/convert.h
+include/vcflib/cigar.hpp
-include/disorder.h
+include/vcflib/convert.h
-include/filevercmp.h
+include/vcflib/disorder.h
-include/gpatInfo.hpp
+include/vcflib/filevercmp.h
-include/join.h
+include/vcflib/gpatInfo.hpp
-include/makeUnique.h
+include/vcflib/join.h
-include/mt19937ar.h
+include/vcflib/legacy.h
-include/multichoose.h
+include/vcflib/makeUnique.h
-include/multipermute.h
+include/vcflib/mt19937ar.h
-include/murmur3.hpp
+include/vcflib/multichoose.h
-include/pdflib.hpp
+include/vcflib/murmur3.hpp
-include/rkmh.hpp
+include/vcflib/pdflib.hpp
-include/rnglib.hpp
+include/vcflib/rkmh.hpp
-include/split.h
+include/vcflib/rnglib.hpp
-include/ssw.hpp
+include/vcflib/split.h
-include/ssw_cpp.hpp
+include/vcflib/ssw.hpp
-include/var.hpp
+include/vcflib/ssw_cpp.hpp
-include/vcf-c-api.h
+include/vcflib/var.hpp
-include/vcf-wfa.h
+include/vcflib/vcf-c-api.h
+include/vcflib/vcf-wfa.h
 lib/libvcflib.a
-%%ZIG%%lib/libzig.a
 lib/pyvcflib%%PYTHON_EXT_SUFFIX%%.so
+%%ZIG%%lib/libzig.a
 share/man/man1/abba-baba.1.gz
 share/man/man1/bFst.1.gz
 share/man/man1/dumpContigsFromHeader.1.gz