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Port details
bcftools Tools for manipulating next-generation sequencing data
1.9 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
Maintainer: cartwright@asu.edu search for ports maintained by this maintainer
Port Added: 05 Jun 2015 21:01:24
License: MIT GPLv3
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/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (42 items)
  1. /usr/local/share/licenses/bcftools-1.9/catalog.mk
  2. /usr/local/share/licenses/bcftools-1.9/LICENSE
  3. /usr/local/share/licenses/bcftools-1.9/MIT
  4. /usr/local/share/licenses/bcftools-1.9/GPLv3
  5. bin/bcftools
  6. bin/color-chrs
  7. bin/guess-ploidy
  8. bin/plot-roh
  9. bin/plot-vcfstats
  10. bin/run-roh
  11. bin/vcfutils
  12. libexec/bcftools/GTisec.so
  13. libexec/bcftools/GTsubset.so
  14. libexec/bcftools/ad-bias.so
  15. libexec/bcftools/af-dist.so
  16. libexec/bcftools/check-ploidy.so
  17. libexec/bcftools/check-sparsity.so
  18. libexec/bcftools/color-chrs.so
  19. libexec/bcftools/contrast.so
  20. libexec/bcftools/counts.so
  21. libexec/bcftools/dosage.so
  22. libexec/bcftools/fill-AN-AC.so
  23. libexec/bcftools/fill-from-fasta.so
  24. libexec/bcftools/fill-tags.so
  25. libexec/bcftools/fixploidy.so
  26. libexec/bcftools/fixref.so
  27. libexec/bcftools/frameshifts.so
  28. libexec/bcftools/guess-ploidy.so
  29. libexec/bcftools/impute-info.so
  30. libexec/bcftools/isecGT.so
  31. libexec/bcftools/mendelian.so
  32. libexec/bcftools/missing2ref.so
  33. libexec/bcftools/prune.so
  34. libexec/bcftools/setGT.so
  35. libexec/bcftools/smpl-stats.so
  36. libexec/bcftools/split.so
  37. libexec/bcftools/tag2tag.so
  38. libexec/bcftools/trio-stats.so
  39. libexec/bcftools/trio-switch-rate.so
  40. man/man1/bcftools.1.gz
  41. @postexec /usr/sbin/service ldconfig restart > /dev/null
  42. @postunexec /usr/sbin/service ldconfig restart > /dev/null
  43. Collapse this list.

To install the port: cd /usr/ports/biology/bcftools/ && make install clean
To add the package: pkg install bcftools

PKGNAME: bcftools

distinfo:

TIMESTAMP = 1532903716
SHA256 (samtools-bcftools-1.9_GH0.tar.gz) = 223b90c9a9b11576174384de70abe8e8394aef1b45c7324e4bf875d0f344e96e
SIZE (samtools-bcftools-1.9_GH0.tar.gz) = 2394968


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. htslib>=1.6 : biology/htslib
  2. autoconf>=2.69 : devel/autoconf
  3. automake>=1.16.1 : devel/automake
  4. gmake : devel/gmake
Library dependencies:
  1. libhts.so : biology/htslib
  2. libgsl.so : math/gsl
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for bcftools-1.9:
     GPL=on: Enable modules that rely on GPL code
===> Use 'make config' to modify these settings

USES:
autoreconf gmake localbase  perl5 python:env shebangfix

Master Sites:
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.9?dummy=/

Number of commits found: 11

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
02 Aug 2018 19:30:57
Original commit files touched by this commit  1.9
Revision:476247
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  1.6_1
Revision:473116
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  1.6
Revision:452840
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  1.3.1_2
Revision:444988
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  1.3.1_1
Revision:439928
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  1.3.1
Revision:415914
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  1.3
Revision:415503
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  1.3
Revision:412344
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  1.3
Revision:404398
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  1.2
Revision:388638
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: 11

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