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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
bcftools Tools for manipulating next-generation sequencing data
1.16 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-06-05 21:01:24
Last Update: 2023-01-05 23:19:22
Commit Hash: adfc943
License: MIT GPLv3
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (55 items)
Collapse this list.
  1. /usr/local/share/licenses/bcftools-1.16/catalog.mk
  2. /usr/local/share/licenses/bcftools-1.16/LICENSE
  3. /usr/local/share/licenses/bcftools-1.16/MIT
  4. /usr/local/share/licenses/bcftools-1.16/GPLv3
  5. bin/bcftools
  6. bin/color-chrs
  7. bin/gff2gff.py
  8. bin/guess-ploidy
  9. bin/plot-roh
  10. bin/plot-vcfstats
  11. bin/run-roh
  12. bin/vcfutils
  13. libexec/bcftools/GTisec.so
  14. libexec/bcftools/GTsubset.so
  15. libexec/bcftools/ad-bias.so
  16. libexec/bcftools/add-variantkey.so
  17. libexec/bcftools/af-dist.so
  18. libexec/bcftools/allele-length.so
  19. libexec/bcftools/check-ploidy.so
  20. libexec/bcftools/check-sparsity.so
  21. libexec/bcftools/color-chrs.so
  22. libexec/bcftools/contrast.so
  23. libexec/bcftools/counts.so
  24. libexec/bcftools/dosage.so
  25. libexec/bcftools/fill-AN-AC.so
  26. libexec/bcftools/fill-from-fasta.so
  27. libexec/bcftools/fill-tags.so
  28. libexec/bcftools/fixploidy.so
  29. libexec/bcftools/fixref.so
  30. libexec/bcftools/frameshifts.so
  31. libexec/bcftools/guess-ploidy.so
  32. libexec/bcftools/gvcfz.so
  33. libexec/bcftools/impute-info.so
  34. libexec/bcftools/indel-stats.so
  35. libexec/bcftools/isecGT.so
  36. libexec/bcftools/mendelian.so
  37. libexec/bcftools/missing2ref.so
  38. libexec/bcftools/parental-origin.so
  39. libexec/bcftools/prune.so
  40. libexec/bcftools/remove-overlaps.so
  41. libexec/bcftools/scatter.so
  42. libexec/bcftools/setGT.so
  43. libexec/bcftools/smpl-stats.so
  44. libexec/bcftools/split-vep.so
  45. libexec/bcftools/split.so
  46. libexec/bcftools/tag2tag.so
  47. libexec/bcftools/trio-dnm2.so
  48. libexec/bcftools/trio-stats.so
  49. libexec/bcftools/trio-switch-rate.so
  50. libexec/bcftools/variant-distance.so
  51. libexec/bcftools/variantkey-hex.so
  52. man/man1/bcftools.1.gz
  53. @owner
  54. @group
  55. @mode
Collapse this list.
Dependency lines:
  • bcftools>0:biology/bcftools
To install the port:
cd /usr/ports/biology/bcftools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bcftools
  • pkg install bcftools
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bcftools
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
bcftools
ABIlatestquarterly
FreeBSD:11:aarch641.91.9_1
FreeBSD:11:amd641.131.12_1
FreeBSD:11:armv61.3.11.9_1
FreeBSD:11:i3861.131.12_1
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips641.3.1pkg-fallout
FreeBSD:12:aarch641.91.15
FreeBSD:12:amd641.161.15
FreeBSD:12:armv61.91.10.2
FreeBSD:12:armv71.91.10.2
FreeBSD:12:i3861.161.15
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips641.9pkg-fallout
FreeBSD:12:powerpc64pkg-fallout1.12
FreeBSD:13:aarch641.161.15
FreeBSD:13:amd641.161.15
FreeBSD:13:armv61.111.15
FreeBSD:13:armv7pkg-fallout1.15
FreeBSD:13:i3861.161.15
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips641.111.11
FreeBSD:13:powerpc641.111.15
FreeBSD:13:riscv64pkg-fallout1.15
FreeBSD:14:aarch641.16pkg-fallout
FreeBSD:14:amd641.16pkg-fallout
FreeBSD:14:armv61.16pkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i3861.16pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc641.15pkg-fallout
FreeBSD:14:riscv641.13pkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. autoconf>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
Test dependencies:
  1. bash : shells/bash
  2. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. bash : shells/bash
Library dependencies:
  1. libhts.so : biology/htslib
  2. libgsl.so : math/gsl
This port is required by:
for Run
  1. biology/bio-mocha
  2. biology/biostar-tools

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message

Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.16?dummy=/
Collapse this list.

Number of commits found: 27

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.16
05 Jan 2023 23:19:22
commit hash:adfc9433b02c9fbd48a51de471dc4f43a22d240fcommit hash:adfc9433b02c9fbd48a51de471dc4f43a22d240fcommit hash:adfc9433b02c9fbd48a51de471dc4f43a22d240fcommit hash:adfc9433b02c9fbd48a51de471dc4f43a22d240f files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.16

New plugin variant-distance to annotate records with distance to the
nearest variant
Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/releases
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.15
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.15
20 Jul 2022 14:20:57
commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671commit hash:37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.15
26 Feb 2022 15:04:10
commit hash:734d2c4df0a562d5be9ef181424ebec5ab7b2222commit hash:734d2c4df0a562d5be9ef181424ebec5ab7b2222commit hash:734d2c4df0a562d5be9ef181424ebec5ab7b2222commit hash:734d2c4df0a562d5be9ef181424ebec5ab7b2222 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.15

Several small enhancements
Changes: https://github.com/samtools/bcftools/releases

Reported by:    portscout
1.14_1
12 Jan 2022 19:41:22
commit hash:654acd81409d31495f8b1b11db61e1afbf640981commit hash:654acd81409d31495f8b1b11db61e1afbf640981commit hash:654acd81409d31495f8b1b11db61e1afbf640981commit hash:654acd81409d31495f8b1b11db61e1afbf640981 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: bump portrevision of consumers after update to 2.7.1

PR:		260201
1.14
18 Dec 2021 17:56:51
commit hash:9302b3e21ff4b44c0003d01b51c648a40ac30ac2commit hash:9302b3e21ff4b44c0003d01b51c648a40ac30ac2commit hash:9302b3e21ff4b44c0003d01b51c648a40ac30ac2commit hash:9302b3e21ff4b44c0003d01b51c648a40ac30ac2 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.14

A few minor enhancements and bug fixes

Changes: https://github.com/samtools/bcftools/tags
1.13
12 Jul 2021 13:30:10
commit hash:94c639f5ff163d57758c0631c7280c9f0fd2e86ecommit hash:94c639f5ff163d57758c0631c7280c9f0fd2e86ecommit hash:94c639f5ff163d57758c0631c7280c9f0fd2e86ecommit hash:94c639f5ff163d57758c0631c7280c9f0fd2e86e files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/bcftools: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/bcftools/releases/tag/1.13
Reported by:    portscout
1.12_1
16 Jun 2021 19:31:27
commit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096ecommit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096e files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
math/gsl: update to 2.7

From [1]

* What is new in gsl-2.7:
	* fixed doc bug for gsl_histogram_min_bin (lhcsky at 163.com)
	* fixed bug #60335 (spmatrix test failure, J. Lamb)
	* fixed bug #36577
	* clarified documentation on interpolation accelerators (V. Krishnan)
	* fixed bug #45521 (erroneous GSL_ERROR_NULL in ode-initval2, thanks to M.
Sitte)
	* fixed doc bug #59758
	* fixed bug #58202 (rstat median for n=5)
	* added support for native C complex number types in gsl_complex
	   when using a C11 compiler
	* upgraded to autoconf 2.71, automake 1.16.3, libtool 2.4.6
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.12
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.12
20 Mar 2021 17:14:32
Revision:568874Original commit files touched by this commit
jwb search for other commits by this committer
biology/htslib: Update to 1.12
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.11

Build-tested all other htslib dependents, no revbumps should be needed

Reported by:    portscout
1.11
05 Nov 2020 20:34:04
Revision:554157Original commit files touched by this commit
jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.11

Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/bcftools/releases/tag/1.11

Reported by:    portscout
1.10.2
03 Aug 2020 18:16:54
Revision:544096Original commit files touched by this commit
jwb search for other commits by this committer
biology/bcftools: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/bcftools/tags

Take maintainership per ports/248089.

PR:             ports/248089
1.9_2
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
jwb search for other commits by this committer
biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089
1.9_1
25 Oct 2019 23:41:34
Revision:515671Original commit files touched by this commit
tcberner search for other commits by this committer
math/gsl: update to 2.6

- math/p5-Math-GSL does not seem to have any upstream activity to make it work
with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
1.9
13 Aug 2019 16:00:39
Revision:508834Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
1.9
02 Aug 2018 19:30:57
Revision:476247Original commit files touched by this commit
fernape search for other commits by this committer
biology/bcftools: update to 1.9

While here:

* Update LICENSE handling
* Move all commands to bin/

PR:	230169
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16543
1.6_1
23 Jun 2018 08:27:14
Revision:473116Original commit files touched by this commit
tcberner search for other commits by this committer
Update math/gsl to 2.5

PR:		229067
04 Dec 2017 15:27:29
Revision:455518 Refresh Original commit files touched by this commit Sanity Test Failure
mat search for other commits by this committer
Add a USES=python:env, that will not add a dependency on Python.

It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.

Sponsored by:	Absolight
1.6
25 Oct 2017 10:19:50
Revision:452840Original commit files touched by this commit
pizzamig search for other commits by this committer
biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768
1.3.1_2
03 Jul 2017 20:38:12
Revision:444988Original commit files touched by this commit
tcberner search for other commits by this committer
Update math/gsl to 2.4

Exp-Run by:	antoine
PR:		220408
1.3.1_1
02 May 2017 05:26:40
Revision:439928Original commit files touched by this commit
tcberner search for other commits by this committer
Update math/gsl to 2.3

This release introduces some new features and fixes several bugs:
	http://savannah.gnu.org/forum/forum.php?forum_id=8751

* update to 2.3 and take maintainership
* update math/py-gsl to 2.2.0 for gsl2 support
* update math/rubygem-rb-gsl to 2.1.0.2 for gsl2 support

PR:		218952
Exp-run by:	antoine
Reviewed by:	mat, rakuco
Approved by:	rakuco (mentor)
Differential Revision:	https://reviews.freebsd.org/D10522
1.3.1
26 May 2016 20:28:55
Revision:415914Original commit files touched by this commit
pi search for other commits by this committer
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)
1.3
19 May 2016 11:09:14
Revision:415503Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
1.3
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
1.3
25 Dec 2015 01:31:09
Revision:404398Original commit files touched by this commit
junovitch search for other commits by this committer
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)
1.2
05 Jun 2015 21:01:14
Revision:388638Original commit files touched by this commit
pi search for other commits by this committer
New port: biology/bcftools

BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.

WWW: http://www.htslib.org/

PR:		199747
Submitted by:	cartwright@asu.edu

Number of commits found: 27