biology/vcflib 1.0.15 FreeBSD

C++ library and CLI tools for parsing and manipulating VCF files

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-10-14
Commit: 3d63dea5e4
License: MIT
Categories: biology
Package size: 2205.5 KiB, 10152.8 KiB installed

Description

The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the defacto standard reporting format for a wide array of genomic variant detectors.

vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both:

an API for parsing and operating on records of genomic variation as it can
be described by the VCF format

and a collection of command-line utilities for executing complex
manipulations on VCF files.

The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users.

In the other systems

System

Port

Version

FreeBSD

biology/vcflib

1.0.15

HardenedBSD

biology/vcflib

1.0.13

GhostBSD

biology/vcflib

1.0.13

Install

Binary package:

pkg install vcflib

From the ports tree:

cd /usr/ports/biology/vcflib/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	vcflib>0:biology/vcflib
LIB_DEPENDS=	libvcflib.so:biology/vcflib

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository	aarch64	amd64	armv6	armv7	i386
FreeBSD:14:latest	1.0.13	1.0.15	1.0.3_1	-	-
FreeBSD:14:quarterly	1.0.13	1.0.15	n/a	-	-
FreeBSD:15:latest	1.0.15	1.0.15	n/a	-	-
FreeBSD:15:quarterly	1.0.15	1.0.15	n/a	n/a	n/a
FreeBSD:16:latest	1.0.13	1.0.15	n/a	n/a	n/a
FreeBSD:16:quarterly	n/a	n/a	n/a	n/a	n/a

Dependencies

As this port's Makefile names them.

Build 2

${PYTHON_PKGNAMEPREFIX}pypandoc>=1.4 : textproc/py-pypandoc
pybind11>0 : devel/pybind11

Library 3

libcurl.so : ftp/curl
libhts.so : biology/htslib
libwfa2.so : biology/wfa2-lib

The full lists below include those, and their dependencies in turn.

Build dependencies 30

Run dependencies 19

Required by 1

biology/freebayes

Configuration

Options name: biology_vcflib

Option

Default

Description

ZIG

off

Use the Zig language implementation

USES: cmake:noninja gmake localbase:ldflags pkgconfig python shebangfix
Service scripts: none
Conflicts with: filevercmp libdisorder

Message after installing

===>   NOTICE:

The vcflib port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

Manual pages 89

abba-baba(1)
bFst(1)
dumpContigsFromHeader(1)
genotypeSummary(1)
hapLrt(1)
iHS(1)
meltEHH(1)
normalize-iHS(1)
pFst(1)
pVst(1)
permuteGPAT++(1)
permuteSmooth(1)
plotHaps(1)
popStats(1)
pyvcflib(1)
segmentFst(1)
segmentIhs(1)
sequenceDiversity(1)
smoother(1)
vcf2dag(1)
vcf2fasta(1)
vcf2tsv(1)
vcfaddinfo(1)
vcfafpath(1)
vcfallelicprimitives(1)
vcfaltcount(1)
vcfannotate(1)
vcfannotategenotypes(1)
vcfbreakmulti(1)
vcfcat(1)
vcfcheck(1)
vcfclassify(1)
vcfcleancomplex(1)
vcfcombine(1)
vcfcommonsamples(1)
vcfcountalleles(1)
vcfcreatemulti(1)
vcfdistance(1)
vcfecho(1)
vcfentropy(1)
vcfevenregions(1)
vcffilter(1)
vcffixup(1)
vcfflatten(1)
vcfgeno2alleles(1)
vcfgeno2haplo(1)
vcfgenosamplenames(1)
vcfgenosummarize(1)
vcfgenotypecompare(1)
vcfgenotypes(1)
vcfglbound(1)
vcfglxgt(1)
vcfhetcount(1)
vcfhethomratio(1)
vcfindex(1)
vcfinfo2qual(1)
vcfinfosummarize(1)
vcfintersect(1)
vcfkeepgeno(1)
vcfkeepinfo(1)
vcfkeepsamples(1)
vcfld(1)
vcfleftalign(1)
vcflength(1)
vcflib(1)
vcflib-api(1)
vcfnulldotslashdot(1)
vcfnullgenofields(1)
vcfnumalt(1)
vcfoverlay(1)
vcfparsealts(1)
vcfprimers(1)
vcfqual2info(1)
vcfrandom(1)
vcfrandomsample(1)
vcfremap(1)
vcfremoveaberrantgenotypes(1)
vcfremovesamples(1)
vcfroc(1)
vcfsample2info(1)
vcfsamplediff(1)
vcfsamplenames(1)
vcfsitesummarize(1)
vcfstats(1)
vcfstreamsort(1)
vcfuniq(1)
vcfuniqalleles(1)
vcfwave(1)
wcFst(1)

pkg-plist 252

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

The first 100 are listed.

distinfo 13

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Commit history 2

Date Commit Credits Log message

2026-10-14

3d63dea5e4

Kenneth Raplee

biology/vcflib: Update to 1.0.15

This updates the Zig dependency to lang/zig015 and fixes the libzig.a build from the undefined __zig_probe_stack bug. Also apply Makefile cleanup and formatting. Approved by: arrowd (co-mentor) Approved by: makc (mentor)

2026-10-08

2414383046

Jason W. Bacon

Release numerous ports to ports@

I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.