./biology/bcftools, Tools for manipulating BCF and VCF variant call files

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Branch: CURRENT, Version: 1.10.2nb1, Package name: bcftools-1.10.2nb1, Maintainer: bacon

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.


Required to run:
[biology/htslib] [lang/python37]

Required to build:
[pkgtools/cwrappers]

Master sites:

SHA1: b19c9ba06b1c8e8f135c1e0ab0e4ff713a291bf4
RMD160: 7713e8c5bd4195eb610544adb26158c16525fdac
Filesize: 2813.471 KB

Version history: (Expand)


CVS history: (Expand)


   2020-08-31 20:13:29 by Thomas Klausner | Files touched by this commit (3631) | Package updated
Log message:
*: bump PKGREVISION for perl-5.32.
   2020-07-27 02:29:04 by Jason Bacon | Files touched by this commit (6)
Log message:
biology/bcftools: Upgrade to 1.10.2

Numerous bug fixes, usability improvements and sanity checks were added since
1.9 to prevent common user errors.
   2020-01-19 00:36:14 by Roland Illig | Files touched by this commit (3046)
Log message:
all: migrate several HOMEPAGEs to https

pkglint --only "https instead of http" -r -F

With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.

This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
   2019-11-02 23:09:01 by Roland Illig | Files touched by this commit (10)
Log message:
biology: align variable assignments

pkglint -Wall -F --only aligned --only indent -r
   2019-08-11 15:25:21 by Thomas Klausner | Files touched by this commit (3557) | Package updated
Log message:
Bump PKGREVISIONs for perl 5.30.0
   2019-04-25 09:33:32 by Maya Rashish | Files touched by this commit (620)
Log message:
PKGREVISION bump for anything using python without a PYPKGPREFIX.

This is a semi-manual PKGREVISION bump.
   2019-03-27 16:58:38 by Jason Bacon | Files touched by this commit (1)
Log message:
biology/bcftools: Add zlib dependency for Linux

Resolves build failures on CentOS
   2018-11-15 10:21:24 by Adam Ciarcinski | Files touched by this commit (4)
Log message:
bcftools: added version 1.9

BCFtools is a program for variant calling and manipulating files 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.
In order to avoid tedious repetion, throughout this document we will use \ 
"VCF"
and "BCF" interchangeably, unless specifically noted.

Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF work in all
situations. Unindexed VCF and BCF and streams work in most, but not all
situations. In general, whenever multiple VCFs are read simultaneously, they
must be indexed and therefore also compressed.