git: 8859320e5667 - main - biology/vcflib: Update to 1.0.3

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Fri, 28 Jan 2022 00:13:37 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=8859320e5667960b2d8d21f1936a21e3e1f0ff3b

commit 8859320e5667960b2d8d21f1936a21e3e1f0ff3b
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2022-01-28 00:09:13 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2022-01-28 00:09:13 +0000

    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