mirror of
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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
This commit is contained in:
Jason W. Bacon
parent
fb684eef54
commit
8859320e56
@ -1,6 +1,6 @@
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PORTNAME= vcflib
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DISTVERSIONPREFIX= v
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DISTVERSION= 1.0.2
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DISTVERSION= 1.0.3
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CATEGORIES= biology
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MAINTAINER= jwb@FreeBSD.org
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@ -11,18 +11,20 @@ LICENSE= MIT
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LIB_DEPENDS= libhts.so:biology/htslib \
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libtabix.so:biology/tabixpp
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USES= cmake localbase:ldflags pkgconfig shebangfix
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USES= cmake localbase:ldflags pkgconfig python shebangfix
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USE_GITHUB= yes
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GH_ACCOUNT= ekg
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GH_TUPLE= ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \
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ekg:multichoose:68733cd:multichoose/multichoose \
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ekg:fastahack:bb33265:fastahack/fastahack \
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ekg:intervaltree:17ddd57:intervaltree/intervaltree \
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ekg:fsom:a6ef318:fsom/fsom \
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GH_TUPLE= ekg:fastahack:bb33265:fastahack/fastahack \
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ekg:filevercmp:1a9b779:filevercmp/filevercmp \
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ekg:fsom:a6ef318:fsom/fsom \
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google:googletest:d225acc:googletest/googletest \
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edawson:libVCFH:615a06b:libVCFH/libVCFH \
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simd-everywhere:simde-no-tests:2931676:simd/src/simde
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ekg:intervaltree:aa59377:intervaltree/intervaltree \
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edawson:libVCFH:44b6580:libVCFH/libVCFH \
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ekg:multichoose:68733cd:multichoose/multichoose \
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ekg:smithwaterman:2610e25:smithwaterman/smithwaterman \
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simd-everywhere:simde-no-tests:9af03cd:simd/src/simde
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SHEBANG_FILES= scripts/*
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# Clang and GCC disable sse2 by default on i386, but it's required for vcflib
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CFLAGS_i386= -msse2
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@ -1,21 +1,21 @@
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TIMESTAMP = 1635902784
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SHA256 (ekg-vcflib-v1.0.2_GH0.tar.gz) = a3ef230864328d96eb3b086bf5bbcc34d6699710c358444621f6c3e3f507c910
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SIZE (ekg-vcflib-v1.0.2_GH0.tar.gz) = 19215813
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SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
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SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
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SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
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SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
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TIMESTAMP = 1643316477
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SHA256 (ekg-vcflib-v1.0.3_GH0.tar.gz) = 5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c
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SIZE (ekg-vcflib-v1.0.3_GH0.tar.gz) = 19213097
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SHA256 (ekg-fastahack-bb33265_GH0.tar.gz) = f671609e1a8d7cacb00065bf307c90c46116af8e5cea939b06edcdbcc6d4bc2a
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SIZE (ekg-fastahack-bb33265_GH0.tar.gz) = 18760
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SHA256 (ekg-intervaltree-17ddd57_GH0.tar.gz) = c2274e2382f893241847f75940ad15bac9d1e122da4416b0d2fc61ebba527ee1
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SIZE (ekg-intervaltree-17ddd57_GH0.tar.gz) = 72488
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SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
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SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
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SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070
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SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053
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SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b
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SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686
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SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa
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SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815
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SHA256 (edawson-libVCFH-615a06b_GH0.tar.gz) = 2774c26c55e1d155fe803b492a745a1d2a3659f4fdbe248d3187ce03edf87223
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SIZE (edawson-libVCFH-615a06b_GH0.tar.gz) = 2295
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SHA256 (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 3877e64f51a7368f768b40167e4cdff36a93d3047f722416581834f1eaf40f63
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SIZE (simd-everywhere-simde-no-tests-2931676_GH0.tar.gz) = 203996
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SHA256 (ekg-intervaltree-aa59377_GH0.tar.gz) = 8d42eee645bcb196da03077c6f567f61529add3a581bb98d85f5c9cfe4b50774
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SIZE (ekg-intervaltree-aa59377_GH0.tar.gz) = 72545
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SHA256 (edawson-libVCFH-44b6580_GH0.tar.gz) = 3c90a6c5f1fbe88bedb4a0dcdc1e55dfa51c58f2acd9b31bceead226ab84785c
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SIZE (edawson-libVCFH-44b6580_GH0.tar.gz) = 2956
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SHA256 (ekg-multichoose-68733cd_GH0.tar.gz) = 909baf2e462e43e71ba0d015fbe759c0ab95331c36d6c4ec65e4a92a7b9d3297
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SIZE (ekg-multichoose-68733cd_GH0.tar.gz) = 6558
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SHA256 (ekg-smithwaterman-2610e25_GH0.tar.gz) = f907becb50945d0858d3bf7a64959905712244cbe8455b35ef1102ff893173ce
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SIZE (ekg-smithwaterman-2610e25_GH0.tar.gz) = 39160
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SHA256 (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 99dcb7d6a2e1dc3f51401ff16eaa5dde93c793e13b514ea9cae4d9819144b8fe
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SIZE (simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz) = 572867
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@ -1,5 +1,7 @@
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bin/abba-baba
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bin/bFst
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bin/bed2region
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bin/bgziptabix
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bin/dumpContigsFromHeader
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bin/genotypeSummary
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bin/hapLrt
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@ -16,22 +18,29 @@ bin/segmentFst
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bin/segmentIhs
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bin/sequenceDiversity
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bin/smoother
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bin/vcf2bed.py
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bin/vcf2dag
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bin/vcf2fasta
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bin/vcf2sqlite.py
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bin/vcf2tsv
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bin/vcf_strip_extra_headers
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bin/vcfaddinfo
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bin/vcfafpath
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bin/vcfallelicprimitives
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bin/vcfaltcount
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bin/vcfannotate
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bin/vcfannotategenotypes
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bin/vcfbiallelic
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bin/vcfbreakmulti
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bin/vcfcat
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bin/vcfcheck
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bin/vcfclassify
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bin/vcfcleancomplex
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bin/vcfclearid
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bin/vcfclearinfo
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bin/vcfcombine
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bin/vcfcommonsamples
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bin/vcfcomplex
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bin/vcfcountalleles
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bin/vcfcreatemulti
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bin/vcfdistance
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@ -39,6 +48,7 @@ bin/vcfecho
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bin/vcfentropy
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bin/vcfevenregions
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bin/vcffilter
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bin/vcffirstheader
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bin/vcffixup
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bin/vcfflatten
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bin/vcfgeno2alleles
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@ -49,37 +59,63 @@ bin/vcfgenotypecompare
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bin/vcfgenotypes
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bin/vcfglbound
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bin/vcfglxgt
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bin/vcfgtcompare.sh
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bin/vcfhetcount
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bin/vcfhethomratio
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bin/vcfindelproximity
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bin/vcfindels
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bin/vcfindex
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bin/vcfinfo2qual
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bin/vcfinfosummarize
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bin/vcfintersect
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bin/vcfjoincalls
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bin/vcfkeepgeno
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bin/vcfkeepinfo
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bin/vcfkeepsamples
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bin/vcfld
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bin/vcfleftalign
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bin/vcflength
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bin/vcfmultiallelic
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bin/vcfmultiway
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bin/vcfmultiwayscripts
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bin/vcfnobiallelicsnps
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bin/vcfnoindels
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bin/vcfnosnps
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bin/vcfnulldotslashdot
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bin/vcfnumalt
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bin/vcfoverlay
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bin/vcfparsealts
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bin/vcfplotaltdiscrepancy.r
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bin/vcfplotaltdiscrepancy.sh
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bin/vcfplotsitediscrepancy.r
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bin/vcfplottstv.sh
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bin/vcfprimers
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bin/vcfprintaltdiscrepancy.r
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bin/vcfprintaltdiscrepancy.sh
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bin/vcfqual2info
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bin/vcfqualfilter
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bin/vcfrandom
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bin/vcfrandomsample
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bin/vcfregionreduce
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bin/vcfregionreduce_and_cut
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bin/vcfregionreduce_pipe
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bin/vcfregionreduce_uncompressed
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bin/vcfremap
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bin/vcfremoveaberrantgenotypes
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bin/vcfremovenonATGC
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bin/vcfremovesamples
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bin/vcfroc
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bin/vcfsample2info
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bin/vcfsamplediff
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bin/vcfsamplenames
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bin/vcfsitesummarize
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bin/vcfsnps
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bin/vcfsort
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bin/vcfstats
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bin/vcfstreamsort
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bin/vcfuniq
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bin/vcfuniqalleles
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bin/vcfvarstats
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bin/wcFst
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include/BandedSmithWaterman.h
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include/BedReader.h
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@ -100,6 +136,7 @@ include/disorder.h
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include/filevercmp.h
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include/gpatInfo.hpp
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include/join.h
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include/makeUnique.h
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include/mt19937ar.h
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include/multichoose.h
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include/multipermute.h
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@ -112,87 +149,88 @@ include/var.hpp
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include/vec128int.h
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include/veclib_types.h
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lib/libvcflib.a
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man/man1/man/abba-baba.1.gz
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man/man1/man/bFst.1.gz
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man/man1/man/dumpContigsFromHeader.1.gz
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man/man1/man/genotypeSummary.1.gz
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man/man1/man/hapLrt.1.gz
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man/man1/man/iHS.1.gz
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man/man1/man/meltEHH.1.gz
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man/man1/man/normalize-iHS.1.gz
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man/man1/man/pFst.1.gz
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man/man1/man/pVst.1.gz
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man/man1/man/permuteGPAT++.1.gz
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man/man1/man/permuteSmooth.1.gz
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man/man1/man/plotHaps.1.gz
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man/man1/man/popStats.1.gz
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man/man1/man/segmentFst.1.gz
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man/man1/man/segmentIhs.1.gz
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man/man1/man/sequenceDiversity.1.gz
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man/man1/man/smoother.1.gz
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man/man1/man/vcf2dag.1.gz
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man/man1/man/vcf2fasta.1.gz
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man/man1/man/vcf2tsv.1.gz
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man/man1/man/vcfaddinfo.1.gz
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man/man1/man/vcfafpath.1.gz
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man/man1/man/vcfallelicprimitives.1.gz
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man/man1/man/vcfaltcount.1.gz
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man/man1/man/vcfannotate.1.gz
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man/man1/man/vcfannotategenotypes.1.gz
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man/man1/man/vcfbreakmulti.1.gz
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man/man1/man/vcfcat.1.gz
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man/man1/man/vcfcheck.1.gz
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man/man1/man/vcfclassify.1.gz
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man/man1/man/vcfcleancomplex.1.gz
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man/man1/man/vcfcombine.1.gz
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man/man1/man/vcfcommonsamples.1.gz
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man/man1/man/vcfcountalleles.1.gz
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man/man1/man/vcfcreatemulti.1.gz
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man/man1/man/vcfdistance.1.gz
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man/man1/man/vcfecho.1.gz
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man/man1/man/vcfentropy.1.gz
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man/man1/man/vcfevenregions.1.gz
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man/man1/man/vcffilter.1.gz
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man/man1/man/vcffixup.1.gz
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man/man1/man/vcfflatten.1.gz
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man/man1/man/vcfgeno2alleles.1.gz
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man/man1/man/vcfgeno2haplo.1.gz
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man/man1/man/vcfgenosamplenames.1.gz
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man/man1/man/vcfgenosummarize.1.gz
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man/man1/man/vcfgenotypecompare.1.gz
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man/man1/man/vcfgenotypes.1.gz
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man/man1/man/vcfglbound.1.gz
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man/man1/man/vcfglxgt.1.gz
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man/man1/man/vcfhetcount.1.gz
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man/man1/man/vcfhethomratio.1.gz
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man/man1/man/vcfindex.1.gz
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man/man1/man/vcfinfo2qual.1.gz
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man/man1/man/vcfinfosummarize.1.gz
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man/man1/man/vcfintersect.1.gz
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man/man1/man/vcfkeepgeno.1.gz
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man/man1/man/vcfkeepinfo.1.gz
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man/man1/man/vcfkeepsamples.1.gz
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man/man1/man/vcfld.1.gz
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man/man1/man/vcfleftalign.1.gz
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man/man1/man/vcflength.1.gz
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man/man1/man/vcflib.1.gz
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man/man1/man/vcfnumalt.1.gz
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man/man1/man/vcfoverlay.1.gz
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man/man1/man/vcfparsealts.1.gz
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man/man1/man/vcfprimers.1.gz
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man/man1/man/vcfqual2info.1.gz
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man/man1/man/vcfrandom.1.gz
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man/man1/man/vcfrandomsample.1.gz
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man/man1/man/vcfremap.1.gz
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man/man1/man/vcfremoveaberrantgenotypes.1.gz
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man/man1/man/vcfremovesamples.1.gz
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man/man1/man/vcfroc.1.gz
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man/man1/man/vcfsample2info.1.gz
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man/man1/man/vcfsamplediff.1.gz
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man/man1/man/vcfsamplenames.1.gz
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man/man1/man/vcfsitesummarize.1.gz
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man/man1/man/vcfstats.1.gz
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man/man1/man/vcfstreamsort.1.gz
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man/man1/man/vcfuniq.1.gz
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man/man1/man/vcfuniqalleles.1.gz
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man/man1/man/wcFst.1.gz
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man/man1/abba-baba.1.gz
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man/man1/bFst.1.gz
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man/man1/dumpContigsFromHeader.1.gz
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man/man1/genotypeSummary.1.gz
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man/man1/hapLrt.1.gz
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man/man1/iHS.1.gz
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man/man1/meltEHH.1.gz
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man/man1/normalize-iHS.1.gz
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man/man1/pFst.1.gz
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man/man1/pVst.1.gz
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man/man1/permuteGPAT++.1.gz
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man/man1/permuteSmooth.1.gz
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man/man1/plotHaps.1.gz
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man/man1/popStats.1.gz
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man/man1/segmentFst.1.gz
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man/man1/segmentIhs.1.gz
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man/man1/sequenceDiversity.1.gz
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man/man1/smoother.1.gz
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man/man1/vcf2dag.1.gz
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man/man1/vcf2fasta.1.gz
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man/man1/vcf2tsv.1.gz
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man/man1/vcfaddinfo.1.gz
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man/man1/vcfafpath.1.gz
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man/man1/vcfallelicprimitives.1.gz
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man/man1/vcfaltcount.1.gz
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man/man1/vcfannotate.1.gz
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man/man1/vcfannotategenotypes.1.gz
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man/man1/vcfbreakmulti.1.gz
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man/man1/vcfcat.1.gz
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man/man1/vcfcheck.1.gz
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man/man1/vcfclassify.1.gz
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man/man1/vcfcleancomplex.1.gz
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man/man1/vcfcombine.1.gz
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man/man1/vcfcommonsamples.1.gz
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man/man1/vcfcountalleles.1.gz
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man/man1/vcfcreatemulti.1.gz
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man/man1/vcfdistance.1.gz
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man/man1/vcfecho.1.gz
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man/man1/vcfentropy.1.gz
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man/man1/vcfevenregions.1.gz
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man/man1/vcffilter.1.gz
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man/man1/vcffixup.1.gz
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man/man1/vcfflatten.1.gz
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man/man1/vcfgeno2alleles.1.gz
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man/man1/vcfgeno2haplo.1.gz
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man/man1/vcfgenosamplenames.1.gz
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man/man1/vcfgenosummarize.1.gz
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man/man1/vcfgenotypecompare.1.gz
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man/man1/vcfgenotypes.1.gz
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man/man1/vcfglbound.1.gz
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man/man1/vcfglxgt.1.gz
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man/man1/vcfhetcount.1.gz
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man/man1/vcfhethomratio.1.gz
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man/man1/vcfindex.1.gz
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man/man1/vcfinfo2qual.1.gz
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man/man1/vcfinfosummarize.1.gz
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man/man1/vcfintersect.1.gz
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man/man1/vcfkeepgeno.1.gz
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man/man1/vcfkeepinfo.1.gz
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man/man1/vcfkeepsamples.1.gz
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||||
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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user