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Port details
bcftools Tools for manipulating next-generation sequencing data
1.3.1_2 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: 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

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

PKGNAME: bcftools

distinfo:

TIMESTAMP = 1463692643
SHA256 (samtools-bcftools-1.3.1_GH0.tar.gz) = 99a5cc05faa974f5ddbeebf346bb51a806bdaaf8e2f6adc3bead28551983e77e
SIZE (samtools-bcftools-1.3.1_GH0.tar.gz) = 958207


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

Build dependencies:
  1. htslib>=1.3 : biology/htslib
  2. 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-1.3.1_2:
     GPL=on: Enable modules that rely on GPL code
===> Use 'make config' to modify these settings

USES:
gmake perl5 shebangfix

Master Sites:
  1. https://codeload.github.com/samtools/bcftools/tar.gz/1.3.1?dummy=/

Number of commits found: 7

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
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: 7

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