Attachment 229250 Details for Bug 259627 – v3

[patch] v3

freebayes.patch (text/plain), 8.38 KB, created by Piotr Kubaj on 2021-11-03 18:05:34 UTC

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Creator: Piotr Kubaj

Created: 2021-11-03 18:05:34 UTC

Size: 8.38 KB

patch

obsolete

>diff f3f7446a00538cc58e3342c0def011efd48593d8 /usr/ports
>blob - ce0cdd503e4187ceee6bb5e2df305f5e077d4488
>file + biology/vcflib/Makefile
>--- biology/vcflib/Makefile
>+++ biology/vcflib/Makefile
>@@ -1,8 +1,6 @@
> PORTNAME=		vcflib
> DISTVERSIONPREFIX=	v
>-DISTVERSION=		1.0.0-rc1-130
>-PORTREVISION=	1
>-DISTVERSIONSUFFIX=	-g7e3d806
>+DISTVERSION=		1.0.2
> CATEGORIES=		biology
> 
> MAINTAINER=	jwb@FreeBSD.org
>@@ -14,43 +12,20 @@ BROKEN_aarch64=		fails to compile: mmintrin.h:47:5: us
> BROKEN_riscv64=		fails to compile: mmintrin.h:47:5: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'?
> 
> LIB_DEPENDS=	libhts.so:biology/htslib \
>-		libtabix.so:biology/tabixpp \
>-		libsw.so:biology/smithwaterman
>-COMMON_DEPENDS=	fastahack:biology/fastahack \
>-		filevercmp:sysutils/filevercmp \
>-		fsom:science/fsom \
>-		multichoose>=1.0.3:math/multichoose \
>-		interval_tree_test:math/intervaltree
>-BUILD_DEPENDS=	${COMMON_DEPENDS}
>-RUN_DEPENDS=	${COMMON_DEPENDS}
>+		libtabix.so:biology/tabixpp
> 
>-USES=		gmake shebangfix
>+USES=		cmake localbase:ldflags pkgconfig shebangfix
> USE_LDCONFIG=	yes
> USE_GITHUB=	yes
> GH_ACCOUNT=	ekg
>+GH_TUPLE=	ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \
>+		ekg:multichoose:68733cd:multichoose/multichoose \
>+		ekg:fastahack:bb33265:fastahack/fastahack \
>+		ekg:intervaltree:17ddd57:intervaltree/intervaltree \
>+		ekg:fsom:a6ef318:fsom/fsom \
>+		ekg:filevercmp:1a9b779:filevercmp/filevercmp \
>+		google:googletest:d225acc:googletest/googletest \
>+		edawson:libVCFH:615a06b:libVCFH/libVCFH \
>+		simd-everywhere:simde-no-tests:2931676:simd/src/simde
> 
>-CXXFLAGS+=	-I${LOCALBASE}/include/smithwaterman \
>-		-I${LOCALBASE}/include/multichoose \
>-		-I${LOCALBASE}/include/filevercmp \
>-		-I${LOCALBASE}/include/fastahack \
>-		-I${LOCALBASE}/include/intervaltree \
>-		-DVERSION='\"${PORTVERSION}\"'
>-
>-# Clang and GCC disable sse2 by default on i386, but it's required for vcflib
>-CFLAGS_i386=	-msse2
>-
>-MAKEFILE=	${FILESDIR}/Makefile.external-libs
>-INSTALL_TARGET=	install-strip
>-
>-.include <bsd.port.options.mk>
>-
>-.if ${ARCH} == powerpc64le
>-CFLAGS+=	-DNO_WARN_X86_INTRINSICS
>-USES+=		compiler:gcc-c++11-lib 
>-.endif
>-
>-post-install:
>-	${RLN} ${STAGEDIR}${PREFIX}/lib/libvcflib.so.1 \
>-		${STAGEDIR}${PREFIX}/lib/libvcflib.so
>-
> .include <bsd.port.mk>
>blob - 985916a8d85be0559c9dc9af8b25ca9ced0b87e3
>file + biology/vcflib/distinfo
>--- biology/vcflib/distinfo
>+++ biology/vcflib/distinfo
>@@ -1,3 +1,21 @@
>-TIMESTAMP = 1523243322
>-SHA256 (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 8ec24354dfc7a87c011c865ab75f3eb72646768ab9cb6eff4263e69763338478
>-SIZE (ekg-vcflib-v1.0.0-rc1-130-g7e3d806_GH0.tar.gz) = 20138644
>+TIMESTAMP = 1635902784
>+SHA256 (ekg-vcflib-v1.0.2_GH0.tar.gz) = a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910
>+SIZE (ekg-vcflib-v1.0.2_GH0.tar.gz) = 19215813
>+SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
>+SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
>+SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
>+SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
>+SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
>+SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
>+SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
>+SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
>+SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
>+SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
>+SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
>+SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
>+SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
>+SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
>+SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
>+SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
>+SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
>+SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
>blob - 944045d78581d1134d262d0d9b2f35943a5354e4
>file + biology/vcflib/pkg-plist
>--- biology/vcflib/pkg-plist
>+++ biology/vcflib/pkg-plist
>@@ -1,4 +1,3 @@
>-bin/LD
> bin/abba-baba
> bin/bFst
> bin/dumpContigsFromHeader
>@@ -59,10 +58,9 @@ bin/vcfintersect
> bin/vcfkeepgeno
> bin/vcfkeepinfo
> bin/vcfkeepsamples
>+bin/vcfld
> bin/vcfleftalign
> bin/vcflength
>-bin/vcfnormalizesvs
>-bin/vcfnull2ref
> bin/vcfnumalt
> bin/vcfoverlay
> bin/vcfparsealts
>@@ -82,23 +80,119 @@ bin/vcfstats
> bin/vcfstreamsort
> bin/vcfuniq
> bin/vcfuniqalleles
>-bin/vcfunphase
> bin/wcFst
>-include/vcflib/BedReader.h
>-include/vcflib/Variant.h
>-include/vcflib/cdflib.hpp
>-include/vcflib/convert.h
>-include/vcflib/gpatInfo.hpp
>-include/vcflib/join.h
>-include/vcflib/mt19937ar.h
>-include/vcflib/pdflib.hpp
>-include/vcflib/rnglib.hpp
>-include/vcflib/split.h
>-include/vcflib/ssw.hpp
>-include/vcflib/ssw_cpp.hpp
>-include/vcflib/var.hpp
>-include/vcflib/vec128int.h
>-include/vcflib/veclib_types.h
>+include/BandedSmithWaterman.h
>+include/BedReader.h
>+include/Fasta.h
>+include/IndelAllele.h
>+include/IntervalTree.h
>+include/LargeFileSupport.h
>+include/LeftAlign.h
>+include/Mosaik.h
>+include/Region.h
>+include/Repeats.h
>+include/SmithWatermanGotoh.h
>+include/Variant.h
>+include/catch.hpp
>+include/cdflib.hpp
>+include/convert.h
>+include/disorder.h
>+include/filevercmp.h
>+include/gpatInfo.hpp
>+include/join.h
>+include/mt19937ar.h
>+include/multichoose.h
>+include/multipermute.h
>+include/pdflib.hpp
>+include/rnglib.hpp
>+include/split.h
>+include/ssw.hpp
>+include/ssw_cpp.hpp
>+include/var.hpp
>+include/vec128int.h
>+include/veclib_types.h
> lib/libvcflib.a
>-lib/libvcflib.so
>-lib/libvcflib.so.1
>+man/man1/man/abba-baba.1.gz
>+man/man1/man/bFst.1.gz
>+man/man1/man/dumpContigsFromHeader.1.gz
>+man/man1/man/genotypeSummary.1.gz
>+man/man1/man/hapLrt.1.gz
>+man/man1/man/iHS.1.gz
>+man/man1/man/meltEHH.1.gz
>+man/man1/man/normalize-iHS.1.gz
>+man/man1/man/pFst.1.gz
>+man/man1/man/pVst.1.gz
>+man/man1/man/permuteGPAT++.1.gz
>+man/man1/man/permuteSmooth.1.gz
>+man/man1/man/plotHaps.1.gz
>+man/man1/man/popStats.1.gz
>+man/man1/man/segmentFst.1.gz
>+man/man1/man/segmentIhs.1.gz
>+man/man1/man/sequenceDiversity.1.gz
>+man/man1/man/smoother.1.gz
>+man/man1/man/vcf2dag.1.gz
>+man/man1/man/vcf2fasta.1.gz
>+man/man1/man/vcf2tsv.1.gz
>+man/man1/man/vcfaddinfo.1.gz
>+man/man1/man/vcfafpath.1.gz
>+man/man1/man/vcfallelicprimitives.1.gz
>+man/man1/man/vcfaltcount.1.gz
>+man/man1/man/vcfannotate.1.gz
>+man/man1/man/vcfannotategenotypes.1.gz
>+man/man1/man/vcfbreakmulti.1.gz
>+man/man1/man/vcfcat.1.gz
>+man/man1/man/vcfcheck.1.gz
>+man/man1/man/vcfclassify.1.gz
>+man/man1/man/vcfcleancomplex.1.gz
>+man/man1/man/vcfcombine.1.gz
>+man/man1/man/vcfcommonsamples.1.gz
>+man/man1/man/vcfcountalleles.1.gz
>+man/man1/man/vcfcreatemulti.1.gz
>+man/man1/man/vcfdistance.1.gz
>+man/man1/man/vcfecho.1.gz
>+man/man1/man/vcfentropy.1.gz
>+man/man1/man/vcfevenregions.1.gz
>+man/man1/man/vcffilter.1.gz
>+man/man1/man/vcffixup.1.gz
>+man/man1/man/vcfflatten.1.gz
>+man/man1/man/vcfgeno2alleles.1.gz
>+man/man1/man/vcfgeno2haplo.1.gz
>+man/man1/man/vcfgenosamplenames.1.gz
>+man/man1/man/vcfgenosummarize.1.gz
>+man/man1/man/vcfgenotypecompare.1.gz
>+man/man1/man/vcfgenotypes.1.gz
>+man/man1/man/vcfglbound.1.gz
>+man/man1/man/vcfglxgt.1.gz
>+man/man1/man/vcfhetcount.1.gz
>+man/man1/man/vcfhethomratio.1.gz
>+man/man1/man/vcfindex.1.gz
>+man/man1/man/vcfinfo2qual.1.gz
>+man/man1/man/vcfinfosummarize.1.gz
>+man/man1/man/vcfintersect.1.gz
>+man/man1/man/vcfkeepgeno.1.gz
>+man/man1/man/vcfkeepinfo.1.gz
>+man/man1/man/vcfkeepsamples.1.gz
>+man/man1/man/vcfld.1.gz
>+man/man1/man/vcfleftalign.1.gz
>+man/man1/man/vcflength.1.gz
>+man/man1/man/vcflib.1.gz
>+man/man1/man/vcfnumalt.1.gz
>+man/man1/man/vcfoverlay.1.gz
>+man/man1/man/vcfparsealts.1.gz
>+man/man1/man/vcfprimers.1.gz
>+man/man1/man/vcfqual2info.1.gz
>+man/man1/man/vcfrandom.1.gz
>+man/man1/man/vcfrandomsample.1.gz
>+man/man1/man/vcfremap.1.gz
>+man/man1/man/vcfremoveaberrantgenotypes.1.gz
>+man/man1/man/vcfremovesamples.1.gz
>+man/man1/man/vcfroc.1.gz
>+man/man1/man/vcfsample2info.1.gz
>+man/man1/man/vcfsamplediff.1.gz
>+man/man1/man/vcfsamplenames.1.gz
>+man/man1/man/vcfsitesummarize.1.gz
>+man/man1/man/vcfstats.1.gz
>+man/man1/man/vcfstreamsort.1.gz
>+man/man1/man/vcfuniq.1.gz
>+man/man1/man/vcfuniqalleles.1.gz
>+man/man1/man/wcFst.1.gz

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Attachments on bug 259627: 229241 | 229245 | 229250 | 229251