diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile
index a42fa6c8898e..7038f110c052 100644
--- a/biology/vcflib/Makefile
+++ b/biology/vcflib/Makefile
@@ -1,36 +1,42 @@
 PORTNAME=		vcflib
 DISTVERSIONPREFIX=	v
-DISTVERSION=		1.0.3
-PORTREVISION=		1
+DISTVERSION=		1.0.5
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
 COMMENT=	C++ library and CLI tools for parsing and manipulating VCF files
 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
 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
@@ -1,21 +1,25 @@
-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
 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-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-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 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
@@ -1,236 +1,250 @@
 bin/abba-baba
 bin/bFst
 bin/bed2region
 bin/bgziptabix
 bin/dumpContigsFromHeader
 bin/genotypeSummary
 bin/hapLrt
 bin/iHS
 bin/meltEHH
 bin/normalize-iHS
 bin/pFst
 bin/pVst
 bin/permuteGPAT++
 bin/permuteSmooth
 bin/plotHaps
 bin/popStats
 bin/segmentFst
 bin/segmentIhs
 bin/sequenceDiversity
 bin/smoother
 bin/vcf2bed.py
 bin/vcf2dag
 bin/vcf2fasta
 bin/vcf2sqlite.py
 bin/vcf2tsv
 bin/vcf_strip_extra_headers
 bin/vcfaddinfo
 bin/vcfafpath
 bin/vcfallelicprimitives
 bin/vcfaltcount
 bin/vcfannotate
 bin/vcfannotategenotypes
 bin/vcfbiallelic
 bin/vcfbreakmulti
 bin/vcfcat
 bin/vcfcheck
 bin/vcfclassify
 bin/vcfcleancomplex
 bin/vcfclearid
 bin/vcfclearinfo
 bin/vcfcombine
 bin/vcfcommonsamples
 bin/vcfcomplex
 bin/vcfcountalleles
 bin/vcfcreatemulti
 bin/vcfdistance
 bin/vcfecho
 bin/vcfentropy
 bin/vcfevenregions
 bin/vcffilter
 bin/vcffirstheader
 bin/vcffixup
 bin/vcfflatten
 bin/vcfgeno2alleles
 bin/vcfgeno2haplo
 bin/vcfgenosamplenames
 bin/vcfgenosummarize
 bin/vcfgenotypecompare
 bin/vcfgenotypes
 bin/vcfglbound
 bin/vcfglxgt
 bin/vcfgtcompare.sh
 bin/vcfhetcount
 bin/vcfhethomratio
 bin/vcfindelproximity
 bin/vcfindels
 bin/vcfindex
 bin/vcfinfo2qual
 bin/vcfinfosummarize
 bin/vcfintersect
 bin/vcfjoincalls
 bin/vcfkeepgeno
 bin/vcfkeepinfo
 bin/vcfkeepsamples
 bin/vcfld
 bin/vcfleftalign
 bin/vcflength
 bin/vcfmultiallelic
 bin/vcfmultiway
 bin/vcfmultiwayscripts
 bin/vcfnobiallelicsnps
 bin/vcfnoindels
 bin/vcfnosnps
 bin/vcfnulldotslashdot
+bin/vcfnullgenofields
 bin/vcfnumalt
 bin/vcfoverlay
 bin/vcfparsealts
 bin/vcfplotaltdiscrepancy.r
 bin/vcfplotaltdiscrepancy.sh
 bin/vcfplotsitediscrepancy.r
 bin/vcfplottstv.sh
 bin/vcfprimers
 bin/vcfprintaltdiscrepancy.r
 bin/vcfprintaltdiscrepancy.sh
 bin/vcfqual2info
 bin/vcfqualfilter
 bin/vcfrandom
 bin/vcfrandomsample
 bin/vcfregionreduce
 bin/vcfregionreduce_and_cut
 bin/vcfregionreduce_pipe
 bin/vcfregionreduce_uncompressed
 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/BedReader.h
 include/Fasta.h
 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
 include/gpatInfo.hpp
 include/join.h
 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
 man/man1/genotypeSummary.1.gz
 man/man1/hapLrt.1.gz
 man/man1/iHS.1.gz
 man/man1/meltEHH.1.gz
 man/man1/normalize-iHS.1.gz
 man/man1/pFst.1.gz
 man/man1/pVst.1.gz
 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
 man/man1/smoother.1.gz
 man/man1/vcf2dag.1.gz
 man/man1/vcf2fasta.1.gz
 man/man1/vcf2tsv.1.gz
 man/man1/vcfaddinfo.1.gz
 man/man1/vcfafpath.1.gz
 man/man1/vcfallelicprimitives.1.gz
 man/man1/vcfaltcount.1.gz
 man/man1/vcfannotate.1.gz
 man/man1/vcfannotategenotypes.1.gz
 man/man1/vcfbreakmulti.1.gz
 man/man1/vcfcat.1.gz
 man/man1/vcfcheck.1.gz
 man/man1/vcfclassify.1.gz
 man/man1/vcfcleancomplex.1.gz
 man/man1/vcfcombine.1.gz
 man/man1/vcfcommonsamples.1.gz
 man/man1/vcfcountalleles.1.gz
 man/man1/vcfcreatemulti.1.gz
 man/man1/vcfdistance.1.gz
 man/man1/vcfecho.1.gz
 man/man1/vcfentropy.1.gz
 man/man1/vcfevenregions.1.gz
 man/man1/vcffilter.1.gz
 man/man1/vcffixup.1.gz
 man/man1/vcfflatten.1.gz
 man/man1/vcfgeno2alleles.1.gz
 man/man1/vcfgeno2haplo.1.gz
 man/man1/vcfgenosamplenames.1.gz
 man/man1/vcfgenosummarize.1.gz
 man/man1/vcfgenotypecompare.1.gz
 man/man1/vcfgenotypes.1.gz
 man/man1/vcfglbound.1.gz
 man/man1/vcfglxgt.1.gz
 man/man1/vcfhetcount.1.gz
 man/man1/vcfhethomratio.1.gz
 man/man1/vcfindex.1.gz
 man/man1/vcfinfo2qual.1.gz
 man/man1/vcfinfosummarize.1.gz
 man/man1/vcfintersect.1.gz
 man/man1/vcfkeepgeno.1.gz
 man/man1/vcfkeepinfo.1.gz
 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
 man/man1/vcfprimers.1.gz
 man/man1/vcfqual2info.1.gz
 man/man1/vcfrandom.1.gz
 man/man1/vcfrandomsample.1.gz
 man/man1/vcfremap.1.gz
 man/man1/vcfremoveaberrantgenotypes.1.gz
 man/man1/vcfremovesamples.1.gz
 man/man1/vcfroc.1.gz
 man/man1/vcfsample2info.1.gz
 man/man1/vcfsamplediff.1.gz
 man/man1/vcfsamplenames.1.gz
 man/man1/vcfsitesummarize.1.gz
 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