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Port details
ad2vcf Add allelic depth info from a SAM stream to a VCF file
0.1.6.19 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 0.1.6_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-03-23 15:15:07
Last Update: 2024-05-19 13:41:41
Commit Hash: f0bca8e
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.
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/ad2vcf
  2. share/man/man1/ad2vcf.1.gz
  3. /usr/local/share/licenses/ad2vcf-0.1.6.19/catalog.mk
  4. /usr/local/share/licenses/ad2vcf-0.1.6.19/LICENSE
  5. /usr/local/share/licenses/ad2vcf-0.1.6.19/BSD2CLAUSE
Collapse this list.
Dependency lines:
  • ad2vcf>0:biology/ad2vcf
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):
ad2vcf
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.1.6.190.1.6.19-0.1.6_10.1.6.19---
FreeBSD:13:quarterly0.1.6_10.1.6_10.1.60.1.6_10.1.6_10.1.60.1.60.1.6
FreeBSD:14:latest0.1.6_10.1.6.190.1.60.1.6_10.1.6.190.1.6-0.1.6
FreeBSD:14:quarterly0.1.6_10.1.6_1-0.1.6_10.1.6_10.1.60.1.60.1.6
FreeBSD:15:latest0.1.6_10.1.6.19n/a0.1.6_1n/a0.1.60.1.60.1.6
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_ad2vcf
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/ad2vcf/tar.gz/0.1.6-19-gf42ae91?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
0.1.6.19
19 May 2024 13:41:41
commit hash: f0bca8e2ac6a1c567df14347582c44c3883b34e4commit hash: f0bca8e2ac6a1c567df14347582c44c3883b34e4commit hash: f0bca8e2ac6a1c567df14347582c44c3883b34e4commit hash: f0bca8e2ac6a1c567df14347582c44c3883b34e4 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 12b1194da2215559ef87e448b94d55a0d2b0a123commit hash: 12b1194da2215559ef87e448b94d55a0d2b0a123commit hash: 12b1194da2215559ef87e448b94d55a0d2b0a123commit hash: 12b1194da2215559ef87e448b94d55a0d2b0a123 files touched by this commit
Nuno Teixeira (eduardo) search for other commits by this committer
biology/ad2vcf: Move man pages to share/man

Approved by:	portmgr (blanket)
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)
0.1.6
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)
0.1.6
11 Jun 2022 14:26:57
commit hash: 5e31c875e135d453a4ef57d0c8a031f0cf96d947commit hash: 5e31c875e135d453a4ef57d0c8a031f0cf96d947commit hash: 5e31c875e135d453a4ef57d0c8a031f0cf96d947commit hash: 5e31c875e135d453a4ef57d0c8a031f0cf96d947 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: eab790a0c7c346d15e074691cd4c764e187d5f91commit hash: eab790a0c7c346d15e074691cd4c764e187d5f91commit hash: eab790a0c7c346d15e074691cd4c764e187d5f91commit hash: eab790a0c7c346d15e074691cd4c764e187d5f91 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: d167ed211d061a3755621789fed9ba3a978d7553commit hash: d167ed211d061a3755621789fed9ba3a978d7553commit hash: d167ed211d061a3755621789fed9ba3a978d7553commit hash: d167ed211d061a3755621789fed9ba3a978d7553 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: b30b9f1a1ec88dba1606442aa02e1cf8e575110ccommit hash: b30b9f1a1ec88dba1606442aa02e1cf8e575110ccommit hash: b30b9f1a1ec88dba1606442aa02e1cf8e575110ccommit hash: b30b9f1a1ec88dba1606442aa02e1cf8e575110c files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: c906bf342e2faaae31004582f1dc16e15d9b1543commit hash: c906bf342e2faaae31004582f1dc16e15d9b1543commit hash: c906bf342e2faaae31004582f1dc16e15d9b1543commit hash: c906bf342e2faaae31004582f1dc16e15d9b1543 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ad2vcf: Remove comment used to silence portlint
0.1.3
11 Jun 2021 15:05:18
commit hash: 874cf7c2593df5d25830b1a6292d0474f8647d5dcommit hash: 874cf7c2593df5d25830b1a6292d0474f8647d5dcommit hash: 874cf7c2593df5d25830b1a6292d0474f8647d5dcommit hash: 874cf7c2593df5d25830b1a6292d0474f8647d5d files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
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
0.1.2
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.
0.1.2
23 Mar 2021 15:15:01
Revision:569033Original commit files touched by this commit
jwb search for other commits by this committer
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.

Number of commits found: 13