diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index f53800bfa2d7..ac8ea593cdfa 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,62 +1,63 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.12 +DISTVERSION= 1.0.13 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 NOT_FOR_ARCHS= armv6 armv7 NOT_FOR_ARCHS_REASON= requires OpenMP which is not supported 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 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:df20dcc:filevercmp/contrib/filevercmp \ ekg:fsom:56695e1:fsom/contrib/fsom \ ekg:intervaltree:aa59377:intervaltree/contrib/intervaltree \ edawson:libVCFH:44b6580:libVCFH/contrib/libVCFH \ ekg:multichoose:e1f94ae:multichoose/contrib/multichoose \ ekg:smithwaterman:2610e25:smithwaterman/contrib/smithwaterman \ simd-everywhere:simde-no-tests:9af03cd:simd/src/simde \ vcflib:tabixpp:ae5cdf8:tabixpp/contrib/tabixpp SHEBANG_FILES= scripts/* # FIXME: Add Zig option + lang/zig dep OPTIONS_DEFINE= ZIG OPTIONS_DEFAULT= OPTIONS_SUB= yes ZIG_DESC= Include Zig language support ZIG_BUILD_DEPENDS= zig>0:lang/zig -CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0 +CMAKE_ARGS+= -DWFA_GITMODULE=OFF -DWFALIB=${LOCALBASE}/lib/libwfa2.so.0 \ + -DTABIXPP_LOCAL=${WRKSRC}/contrib/tabixpp ZIG_CMAKE_OFF= -DZIG=OFF # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 # filevercmp is deprecated. Remove conflict when the port is removed. CONFLICTS_INSTALL= filevercmp libdisorder # include/disorder.h include/filevercmp.h include/pdflib.hpp .include post-stage: ${MV} ${STAGEDIR}${PREFIX}/bin/libvcflib.a ${STAGEDIR}${PREFIX}/lib .if ${PORT_OPTIONS:MZIG} ${MV} ${STAGEDIR}/usr/lib/libzig.a ${STAGEDIR}${PREFIX}/lib .endif .include diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index 066030757d4d..f9a114d02cf4 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,21 +1,21 @@ -TIMESTAMP = 1732541764 -SHA256 (ekg-vcflib-v1.0.12_GH0.tar.gz) = 7ab5b6a87a39105107029f5e0da52ece612c71095ab2aec69a00320f44bc5300 -SIZE (ekg-vcflib-v1.0.12_GH0.tar.gz) = 23543176 +TIMESTAMP = 1745795908 +SHA256 (ekg-vcflib-v1.0.13_GH0.tar.gz) = ea062b6cf6b9074118bc949112b4f0d3fcc5edb58af9621f9acb92f08a452c55 +SIZE (ekg-vcflib-v1.0.13_GH0.tar.gz) = 23544091 SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760 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-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-ae5cdf8_GH0.tar.gz) = edb15012b57c6bfc900c1b8275fc3d55f2e7c21e83601f8cfedcbdf3107fbb04 SIZE (vcflib-tabixpp-ae5cdf8_GH0.tar.gz) = 6965 diff --git a/biology/vcflib/files/patch-CMakeLists.txt b/biology/vcflib/files/patch-CMakeLists.txt index 347b5a48ab73..695ac3940fd3 100644 --- a/biology/vcflib/files/patch-CMakeLists.txt +++ b/biology/vcflib/files/patch-CMakeLists.txt @@ -1,22 +1,24 @@ ---- CMakeLists.txt.orig 2024-11-21 07:59:50 UTC +--- CMakeLists.txt.orig 2025-04-24 23:28:09 UTC +++ CMakeLists.txt -@@ -70,7 +70,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) +@@ -68,7 +68,7 @@ if (${CMAKE_BUILD_TYPE} MATCHES Release) endif() if (${CMAKE_BUILD_TYPE} MATCHES Release) - set(EXTRA_FLAGS "-march=native -D_FILE_OFFSET_BITS=64") + set(EXTRA_FLAGS "-D_FILE_OFFSET_BITS=64") # set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast endif() -@@ -595,8 +595,8 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS +@@ -590,9 +590,9 @@ install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INS # ---- Install install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) --install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) -+# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) +-if(WFA_GITMODULE) +- install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) +-endif(WFA_GITMODULE) ++# if(WFA_GITMODULE) ++# install(TARGETS ${WFALIB} ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) ++# endif(WFA_GITMODULE) 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) diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 85671a488441..d5e562de28bf 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -1,244 +1,251 @@ 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/vcflib/BandedSmithWaterman.h include/vcflib/BedReader.h include/vcflib/Fasta.h include/vcflib/IndelAllele.h include/vcflib/IntervalTree.h include/vcflib/LargeFileSupport.h include/vcflib/LeftAlign.h include/vcflib/LeftAlign.hpp include/vcflib/Mosaik.h include/vcflib/Region.h include/vcflib/Repeats.h include/vcflib/SmithWatermanGotoh.h include/vcflib/Variant.h include/vcflib/allele.hpp -include/vcflib/canonicalize.h include/vcflib/catch.hpp include/vcflib/cdflib.hpp include/vcflib/cigar.hpp include/vcflib/convert.h include/vcflib/disorder.h include/vcflib/filevercmp.h include/vcflib/gpatInfo.hpp +include/vcflib/index.hpp include/vcflib/join.h include/vcflib/legacy.h -include/vcflib/makeUnique.h include/vcflib/mt19937ar.h include/vcflib/multichoose.h include/vcflib/murmur3.hpp include/vcflib/pdflib.hpp +include/vcflib/phase.hpp include/vcflib/rkmh.hpp include/vcflib/rnglib.hpp include/vcflib/split.h include/vcflib/ssw.hpp include/vcflib/ssw_cpp.hpp +include/vcflib/stats.hpp +include/vcflib/tabix.hpp include/vcflib/var.hpp include/vcflib/vcf-c-api.h include/vcflib/vcf-wfa.h lib/libvcflib.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 share/man/man1/genotypeSummary.1.gz share/man/man1/hapLrt.1.gz share/man/man1/iHS.1.gz share/man/man1/meltEHH.1.gz share/man/man1/normalize-iHS.1.gz share/man/man1/pFst.1.gz share/man/man1/pVst.1.gz share/man/man1/permuteGPAT++.1.gz share/man/man1/permuteSmooth.1.gz share/man/man1/plotHaps.1.gz share/man/man1/popStats.1.gz share/man/man1/pyvcflib.1.gz share/man/man1/segmentFst.1.gz share/man/man1/segmentIhs.1.gz share/man/man1/sequenceDiversity.1.gz share/man/man1/smoother.1.gz share/man/man1/vcf2dag.1.gz share/man/man1/vcf2fasta.1.gz share/man/man1/vcf2tsv.1.gz share/man/man1/vcfaddinfo.1.gz share/man/man1/vcfafpath.1.gz share/man/man1/vcfallelicprimitives.1.gz share/man/man1/vcfaltcount.1.gz share/man/man1/vcfannotate.1.gz share/man/man1/vcfannotategenotypes.1.gz share/man/man1/vcfbreakmulti.1.gz share/man/man1/vcfcat.1.gz share/man/man1/vcfcheck.1.gz share/man/man1/vcfclassify.1.gz share/man/man1/vcfcleancomplex.1.gz share/man/man1/vcfcombine.1.gz share/man/man1/vcfcommonsamples.1.gz share/man/man1/vcfcountalleles.1.gz share/man/man1/vcfcreatemulti.1.gz share/man/man1/vcfdistance.1.gz share/man/man1/vcfecho.1.gz share/man/man1/vcfentropy.1.gz share/man/man1/vcfevenregions.1.gz share/man/man1/vcffilter.1.gz share/man/man1/vcffixup.1.gz share/man/man1/vcfflatten.1.gz share/man/man1/vcfgeno2alleles.1.gz share/man/man1/vcfgeno2haplo.1.gz share/man/man1/vcfgenosamplenames.1.gz share/man/man1/vcfgenosummarize.1.gz share/man/man1/vcfgenotypecompare.1.gz share/man/man1/vcfgenotypes.1.gz share/man/man1/vcfglbound.1.gz share/man/man1/vcfglxgt.1.gz share/man/man1/vcfhetcount.1.gz share/man/man1/vcfhethomratio.1.gz share/man/man1/vcfindex.1.gz share/man/man1/vcfinfo2qual.1.gz share/man/man1/vcfinfosummarize.1.gz share/man/man1/vcfintersect.1.gz share/man/man1/vcfkeepgeno.1.gz share/man/man1/vcfkeepinfo.1.gz share/man/man1/vcfkeepsamples.1.gz share/man/man1/vcfld.1.gz share/man/man1/vcfleftalign.1.gz share/man/man1/vcflength.1.gz share/man/man1/vcflib-api.1.gz share/man/man1/vcflib.1.gz share/man/man1/vcfnulldotslashdot.1.gz share/man/man1/vcfnullgenofields.1.gz share/man/man1/vcfnumalt.1.gz share/man/man1/vcfoverlay.1.gz share/man/man1/vcfparsealts.1.gz share/man/man1/vcfprimers.1.gz share/man/man1/vcfqual2info.1.gz share/man/man1/vcfrandom.1.gz share/man/man1/vcfrandomsample.1.gz share/man/man1/vcfremap.1.gz share/man/man1/vcfremoveaberrantgenotypes.1.gz share/man/man1/vcfremovesamples.1.gz share/man/man1/vcfroc.1.gz share/man/man1/vcfsample2info.1.gz share/man/man1/vcfsamplediff.1.gz share/man/man1/vcfsamplenames.1.gz share/man/man1/vcfsitesummarize.1.gz share/man/man1/vcfstats.1.gz share/man/man1/vcfstreamsort.1.gz share/man/man1/vcfuniq.1.gz share/man/man1/vcfuniqalleles.1.gz share/man/man1/vcfwave.1.gz share/man/man1/wcFst.1.gz