From 8859320e5667960b2d8d21f1936a21e3e1f0ff3b Mon Sep 17 00:00:00 2001 From: "Jason W. Bacon" Date: Thu, 27 Jan 2022 18:09:13 -0600 Subject: [PATCH] biology/vcflib: Update to 1.0.3 Several new commands A few bug fixes and enhancements Changes: https://github.com/vcflib/vcflib/tags Reported by: portscout --- biology/vcflib/Makefile | 20 ++-- biology/vcflib/distinfo | 30 +++--- biology/vcflib/pkg-plist | 206 +++++++++++++++++++++++---------------- 3 files changed, 148 insertions(+), 108 deletions(-) diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 831874e18fdf..4bc5f9a9d945 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -1,6 +1,6 @@ PORTNAME= vcflib DISTVERSIONPREFIX= v -DISTVERSION= 1.0.2 +DISTVERSION= 1.0.3 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org @@ -11,18 +11,20 @@ LICENSE= MIT LIB_DEPENDS= libhts.so:biology/htslib \ libtabix.so:biology/tabixpp -USES= cmake localbase:ldflags pkgconfig shebangfix +USES= cmake localbase:ldflags pkgconfig python shebangfix 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 \ +GH_TUPLE= ekg:fastahack:bb33265:fastahack/fastahack \ ekg:filevercmp:1a9b779:filevercmp/filevercmp \ + ekg:fsom:a6ef318:fsom/fsom \ google:googletest:d225acc:googletest/googletest \ - edawson:libVCFH:615a06b:libVCFH/libVCFH \ - simd-everywhere:simde-no-tests:2931676:simd/src/simde + 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 +SHEBANG_FILES= scripts/* # Clang and GCC disable sse2 by default on i386, but it's required for vcflib CFLAGS_i386= -msse2 diff --git a/biology/vcflib/distinfo b/biology/vcflib/distinfo index 6483bb55115d..bdbfdb931717 100644 --- a/biology/vcflib/distinfo +++ b/biology/vcflib/distinfo @@ -1,21 +1,21 @@ -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 +TIMESTAMP = 1643316477 +SHA256 (ekg-vcflib-v1.0.3_GH0.tar.gz) = 5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c +SIZE (ekg-vcflib-v1.0.3_GH0.tar.gz) = 19213097 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 (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 (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 +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 diff --git a/biology/vcflib/pkg-plist b/biology/vcflib/pkg-plist index 4aa9ba414bd3..14fd56d8448f 100644 --- a/biology/vcflib/pkg-plist +++ b/biology/vcflib/pkg-plist @@ -1,5 +1,7 @@ bin/abba-baba bin/bFst +bin/bed2region +bin/bgziptabix bin/dumpContigsFromHeader bin/genotypeSummary bin/hapLrt @@ -16,22 +18,29 @@ 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 @@ -39,6 +48,7 @@ bin/vcfecho bin/vcfentropy bin/vcfevenregions bin/vcffilter +bin/vcffirstheader bin/vcffixup bin/vcfflatten bin/vcfgeno2alleles @@ -49,37 +59,63 @@ 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/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/wcFst include/BandedSmithWaterman.h include/BedReader.h @@ -100,6 +136,7 @@ include/disorder.h include/filevercmp.h include/gpatInfo.hpp include/join.h +include/makeUnique.h include/mt19937ar.h include/multichoose.h include/multipermute.h @@ -112,87 +149,88 @@ include/var.hpp include/vec128int.h include/veclib_types.h lib/libvcflib.a -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 +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/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.1.gz +man/man1/vcfnulldotslashdot.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/wcFst.1.gz