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Port details
vcf-split Split a multi-sample VCF into single-sample VCFs
0.1.5.10_1 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 0.1.5.10Version 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: 2024-03-02 20:04:57
Commit Hash: 0a569bf
License: BSD2CLAUSE
WWW:
https://github.com/auerlab/vcf-split
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (5 items)
Collapse this list.
  1. bin/vcf-split
  2. share/man/man1/vcf-split.1.gz
  3. /usr/local/share/licenses/vcf-split-0.1.5.10_1/catalog.mk
  4. /usr/local/share/licenses/vcf-split-0.1.5.10_1/LICENSE
  5. /usr/local/share/licenses/vcf-split-0.1.5.10_1/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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: vcf-split
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1694019194 SHA256 (auerlab-vcf-split-0.1.5-10-g0f2fd0a_GH0.tar.gz) = d29d14a233ddd0bbaf1ea33179aaff073b4e991ca96b4572f7b72a00cdea94f2 SIZE (auerlab-vcf-split-0.1.5-10-g0f2fd0a_GH0.tar.gz) = 22576

Packages (timestamps in pop-ups are UTC):
vcf-split
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.1.5.10_10.1.5.10_1-0.1.5.10_10.1.5.10_1---
FreeBSD:13:quarterly0.1.5.100.1.5.100.1.5.40.1.5.100.1.5.100.1.5.100.1.5.100.1.5.10
FreeBSD:14:latest0.1.5.10_10.1.5.10_10.1.5.40.1.5.100.1.5.10_10.1.5.4-0.1.5.4
FreeBSD:14:quarterly0.1.5.100.1.5.10-0.1.5.100.1.5.100.1.5.100.1.5.100.1.5.10
FreeBSD:15:latest0.1.5.10_10.1.5.10_1n/a0.1.5.10n/a0.1.5.100.1.5.100.1.5.10
FreeBSD:15:quarterly--n/a-n/a---
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:
No options to configure
Options name:
biology_vcf-split
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/auerlab/vcf-split/tar.gz/0.1.5-10-g0f2fd0a?dummy=/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.1.5.10_1
02 Mar 2024 20:04:57
commit hash: 0a569bfa8a91916320cc62fa314867aa2cb70c49commit hash: 0a569bfa8a91916320cc62fa314867aa2cb70c49commit hash: 0a569bfa8a91916320cc62fa314867aa2cb70c49commit hash: 0a569bfa8a91916320cc62fa314867aa2cb70c49 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/vcf-split: Move man pages to share/man

Approved by:	portmgr (blanket)
0.1.5.10
28 Oct 2023 11:41:39
commit hash: 1d29500ebc10cfea8cc83bbadd14bbf49e266039commit hash: 1d29500ebc10cfea8cc83bbadd14bbf49e266039commit hash: 1d29500ebc10cfea8cc83bbadd14bbf49e266039commit hash: 1d29500ebc10cfea8cc83bbadd14bbf49e266039 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.5.10

Updates for new libxtend API
0.1.5.4
11 Dec 2022 20:11:33
commit hash: 73209dc866d5c2d7a77a2b307043944266615492commit hash: 73209dc866d5c2d7a77a2b307043944266615492commit hash: 73209dc866d5c2d7a77a2b307043944266615492commit hash: 73209dc866d5c2d7a77a2b307043944266615492 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.5-4

Update for biolibc API changes
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.1.5
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.1.5
11 Jun 2022 14:26:56
commit hash: ef8583e1d5f3c4fbdbda5d15a8deaa50334a22f1commit hash: ef8583e1d5f3c4fbdbda5d15a8deaa50334a22f1commit hash: ef8583e1d5f3c4fbdbda5d15a8deaa50334a22f1commit hash: ef8583e1d5f3c4fbdbda5d15a8deaa50334a22f1 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.5

Use stremalined biolibc API
Minor build system improvements

Changes:        https://github.com/auerlab/vcf-split/tags
0.1.4
15 Mar 2022 21:43:40
commit hash: 58a9101d2b9cc8b8d7e9a29243f0da8910f5d6bfcommit hash: 58a9101d2b9cc8b8d7e9a29243f0da8910f5d6bfcommit hash: 58a9101d2b9cc8b8d7e9a29243f0da8910f5d6bfcommit hash: 58a9101d2b9cc8b8d7e9a29243f0da8910f5d6bf files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.4

Minor update for biolibc 0.2.2 API changes
0.1.3.3
14 Dec 2021 19:45:32
commit hash: 300dbd1c83fd35824efff639b18c0a0ddb7364a1commit hash: 300dbd1c83fd35824efff639b18c0a0ddb7364a1commit hash: 300dbd1c83fd35824efff639b18c0a0ddb7364a1commit hash: 300dbd1c83fd35824efff639b18c0a0ddb7364a1 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.3.3

Transfer header from multi-sample input
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements
0.1.2.14
28 Aug 2021 01:30:52
commit hash: 61ebfe4137ea5de2b6d514f215b7a787f4ca4761commit hash: 61ebfe4137ea5de2b6d514f215b7a787f4ca4761commit hash: 61ebfe4137ea5de2b6d514f215b7a787f4ca4761commit hash: 61ebfe4137ea5de2b6d514f215b7a787f4ca4761 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/vcf-split: Update to 0.1.2.14

Updates for libxtend and biolibc API changes
0.1.2
11 Jun 2021 15:05:19
commit hash: f2ef77c8ce9e5b4bf09024624d0716b124b07a10commit hash: f2ef77c8ce9e5b4bf09024624d0716b124b07a10commit hash: f2ef77c8ce9e5b4bf09024624d0716b124b07a10commit hash: f2ef77c8ce9e5b4bf09024624d0716b124b07a10 files touched by this commit
Jason W. Bacon (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
0.1.1
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.1.1
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.1.1
21 Mar 2021 15:17:28
Revision:568922Original commit files touched by this commit
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: 13