| Port details |
- ad2vcf Add allelic depth info from a SAM stream to a VCF file
- 0.1.6.19 biology
 =2      0.1.6.19Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-03-23 15:15:07
- Last Update: 2024-05-19 13:41:41
- Commit Hash: f0bca8e
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: BSD2CLAUSE
- WWW:
- https://github.com/auerlab/ad2vcf
- Description:
- ad2vcf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- To install the port:
- cd /usr/ports/biology/ad2vcf/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/ad2vcf
- pkg install ad2vcf
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: ad2vcf
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1716122785
SHA256 (auerlab-ad2vcf-0.1.6-19-gf42ae91_GH0.tar.gz) = d71a584e8b74e853a8595ddfa7327959b2fc991b5c6034e9402024384e7a1297
SIZE (auerlab-ad2vcf-0.1.6-19-gf42ae91_GH0.tar.gz) = 16176
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_ad2vcf
- 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 |
|---|
0.1.6.19
19 May 2024 13:41:41
 |
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.6.19
Use xt_fopen() to support all common compression tools
A few other minor improvements |
0.1.6_1
02 Mar 2024 18:32:34
|
Nuno Teixeira (eduardo) |
biology/ad2vcf: Move man pages to share/man
Approved by: portmgr (blanket) |
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) |
0.1.6
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  ) |
0.1.6
11 Jun 2022 14:26:57
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.6
Updates for bl_sam_t and bl_vcf_t API streamlining
Changes: https://github.com/auerlab/ad2vcf/tags |
0.1.5
15 Mar 2022 21:39:32
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.5
Minor update for bioloibc 0.2.2 API changes |
0.1.4
14 Dec 2021 19:45:31
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.4
Updates for evolving libxtend and biolibc APIs
Add --version flag
Filter out unused SAM fields on input
Numerous other minor fixes and enhancements
Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4 |
0.1.3.31
28 Aug 2021 01:28:10
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.3.31
Updates for libxtend and biolibc API changes
Clean up and minor bug fixes |
0.1.3
11 Jun 2021 15:39:02
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Remove comment used to silence portlint |
0.1.3
11 Jun 2021 15:05:18
|
Jason W. Bacon (jwb) |
biology/ad2vcf: Update to 0.1.3
Updates for new biolibc API
Changes: https://github.com/auerlab/ad2vcf/releases |
0.1.2
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.2
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.2
23 Mar 2021 15:15:01
 |
jwb |
biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file
ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file. SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process. |
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