notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Port details
vcf-split Split a multi-sample VCF into single-sample VCFs
0.1.2 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 View this port on Repology. pkg-fallout 0.1.1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-21 15:17:34
Last Update: 2021-06-11 15:05:19
Commit Hash: f2ef77c
License: BSD2CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/vcf-split
  2. man/man1/vcf-split.1.gz
  3. /usr/local/share/licenses/vcf-split-0.1.2/catalog.mk
  4. /usr/local/share/licenses/vcf-split-0.1.2/LICENSE
  5. /usr/local/share/licenses/vcf-split-0.1.2/BSD2CLAUSE
Collapse this list.
Dependency lines:
  • vcf-split>0:biology/vcf-split
To install the port: cd /usr/ports/biology/vcf-split/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/vcf-split
  • pkg install vcf-split
PKGNAME: vcf-split
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
vcf-split
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd640.1.20.1.1
FreeBSD:11:armv6--
FreeBSD:11:i3860.1.20.1.1
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-0.1.1
FreeBSD:12:amd640.1.20.1.1
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3860.1.20.1.1
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-0.1.1
FreeBSD:13:aarch64-0.1.1
FreeBSD:13:amd640.1.20.1.1
FreeBSD:13:armv6-0.1.1
FreeBSD:13:armv7-0.1.1
FreeBSD:13:i3860.1.20.1.1
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64-0.1.1
FreeBSD:14:aarch640.1.2-
FreeBSD:14:amd640.1.2-
FreeBSD:14:armv60.1.1-
FreeBSD:14:armv70.1.1-
FreeBSD:14:i3860.1.2-
FreeBSD:14:mips--
FreeBSD:14:mips640.1.2-
FreeBSD:14:powerpc640.1.1-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Library dependencies:
  1. libbiolibc.so : biology/biolibc
  2. libxtend.so : devel/libxtend
There are no ports dependent upon this port

Configuration Options:
Options name:
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/auerlab/vcf-split/tar.gz/0.1.2?dummy=/
Collapse this list.

Number of commits found: 4

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
11 Jun 2021 15:05:19
 files touched by this commit commit hash:f2ef77c8ce9e5b4bf09024624d0716b124b07a10  0.1.2
jwb search for other commits by this committer
biology/vcf-split: Update to 0.1.2

Updates for new biolibc API

Changes:        https://github.com/auerlab/vcf-split/releases
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.1.1
mat search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.1.1
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
21 Mar 2021 15:17:28
Original commit files touched by this commit Revision:568922  0.1.1
jwb search for other commits by this committer
biology/vcf-split: Split a multi-sample VCF into single-sample VCFs

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.

Number of commits found: 4