| Port details |
- vcf-split Split a multi-sample VCF into single-sample VCFs
- 0.1.5.10_1 biology
 =2      0.1.5.10_1Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-03-21 15:17:34
- Last Update: 2024-03-02 20:04:57
- Commit Hash: 0a569bf
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Library dependencies:
-
- libbiolibc.so : biology/biolibc
- libxtend.so : devel/libxtend
- This port is required by:
- for Run
-
- biology/mca-calling
Configuration Options:- No options to configure
- Options name:
- biology_vcf-split
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.1.5.10_1
02 Mar 2024 20:04:57
 |
Nuno Teixeira (eduardo) |
biology/vcf-split: Move man pages to share/man
Approved by: portmgr (blanket) |
0.1.5.10
28 Oct 2023 11:41:39
|
Jason W. Bacon (jwb) |
biology/vcf-split: Update to 0.1.5.10
Updates for new libxtend API |
0.1.5.4
11 Dec 2022 20:11:33
|
Jason W. Bacon (jwb) |
biology/vcf-split: Update to 0.1.5-4
Update for biolibc API changes |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
0.1.5
11 Jun 2022 14:26:56
|
Jason W. Bacon (jwb) |
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
|
Jason W. Bacon (jwb) |
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
|
Jason W. Bacon (jwb) |
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
|
Jason W. Bacon (jwb) |
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
|
Jason W. Bacon (jwb) |
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
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.1
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.1
21 Mar 2021 15:17:28
 |
jwb |
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. |
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