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Port details
bcftools Tools for manipulating next-generation sequencing data
1.13 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 1.13Version 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: 2021-07-12 13:30:10
Commit Hash: 94c639f
License: MIT GPLv3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (54 items)
Collapse this list.
  1. /usr/local/share/licenses/bcftools-1.13/catalog.mk
  2. /usr/local/share/licenses/bcftools-1.13/LICENSE
  3. /usr/local/share/licenses/bcftools-1.13/MIT
  4. /usr/local/share/licenses/bcftools-1.13/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/variantkey-hex.so
  51. man/man1/bcftools.1.gz
  52. @owner
  53. @group
  54. @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
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:mips--
FreeBSD:11:mips641.3.1-
FreeBSD:12:aarch641.91.13
FreeBSD:12:amd641.131.13
FreeBSD:12:armv61.91.10.2
FreeBSD:12:armv71.91.10.2
FreeBSD:12:i3861.131.13
FreeBSD:12:mips--
FreeBSD:12:mips641.9-
FreeBSD:12:powerpc64-1.12
FreeBSD:13:aarch641.111.13
FreeBSD:13:amd641.131.13
FreeBSD:13:armv61.111.12
FreeBSD:13:armv71.111.12
FreeBSD:13:i3861.131.13
FreeBSD:13:mips--
FreeBSD:13:mips641.111.11
FreeBSD:13:powerpc641.111.12_1
FreeBSD:14:aarch641.13-
FreeBSD:14:amd641.13-
FreeBSD:14:armv61.12-
FreeBSD:14:armv71.12-
FreeBSD:14:i3861.13-
FreeBSD:14:mips--
FreeBSD:14:mips641.13-
FreeBSD:14:powerpc641.12-
 

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>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
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/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/1.13?dummy=/
Collapse this list.

Number of commits found: 20

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
12 Jul 2021 13:30:10
 files touched by this commit commit hash:94c639f5ff163d57758c0631c7280c9f0fd2e86e  1.13
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
16 Jun 2021 19:31:27
 files touched by this commit commit hash:63e653adaa7493aa98f17f9fbc834c0aed7e096e  1.12_1
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)
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  1.12
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
20 Mar 2021 17:14:32
Original commit files touched by this commit Revision:568874  1.12
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
05 Nov 2020 20:34:04
Original commit files touched by this commit Revision:554157  1.11
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
03 Aug 2020 18:16:54
Original commit files touched by this commit Revision:544096  1.10.2
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
03 Aug 2020 17:40:04
Original commit files touched by this commit Revision:544090  1.9_2
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
25 Oct 2019 23:41:34
Original commit files touched by this commit Revision:515671  1.9_1
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
13 Aug 2019 16:00:39
Original commit files touched by this commit Revision:508834  1.9
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories a-c)
02 Aug 2018 19:30:57
Original commit files touched by this commit Revision:476247  1.9
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
23 Jun 2018 08:27:14
Original commit files touched by this commit Revision:473116  1.6_1
tcberner search for other commits by this committer
Update math/gsl to 2.5

PR:		229067
04 Dec 2017 15:27:29
Refresh Original commit files touched by this commit Revision:455518  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
25 Oct 2017 10:19:50
Original commit files touched by this commit Revision:452840  1.6
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
03 Jul 2017 20:38:12
Original commit files touched by this commit Revision:444988  1.3.1_2
tcberner search for other commits by this committer
Update math/gsl to 2.4

Exp-Run by:	antoine
PR:		220408
02 May 2017 05:26:40
Original commit files touched by this commit Revision:439928  1.3.1_1
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
26 May 2016 20:28:55
Original commit files touched by this commit Revision:415914  1.3.1
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)
19 May 2016 11:09:14
Original commit files touched by this commit Revision:415503  1.3
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-messages

Approved by:	portmgr blanket
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  1.3
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
25 Dec 2015 01:31:09
Original commit files touched by this commit Revision:404398  1.3
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)
05 Jun 2015 21:01:14
Original commit files touched by this commit Revision:388638  1.2
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: 20