| Port details |
- bamutil Utilities for working with SAM/BAM files
- 1.0.15 biology
 =2      1.0.15Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2021-10-12 16:45:03
- Last Update: 2022-09-07 21:58:51
- Commit Hash: fb16dfe
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv3
- WWW:
- https://github.com/statgen/bamUtil
- Description:
- Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health. It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- bamutil>0:biology/bamutil
- Conflicts:
- CONFLICTS_INSTALL:
- To install the port:
- cd /usr/ports/biology/bamutil/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/bamutil
- pkg install bamutil
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: bamutil
- Flavors: there is no flavor information for this port.
- distinfo:
- TIMESTAMP = 1634754069
SHA256 (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 24ac4bdb81eded6e33f60dba85ec3d32ebdb06d42f75df775c2632bbfbd8cce9
SIZE (statgen-bamUtil-v1.0.15_GH0.tar.gz) = 1929150
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- This port is required by:
- for Run
-
- biology/biostar-tools
Configuration Options:- No options to configure
- Options name:
- biology_bamutil
- USES:
- gmake
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Number of commits found: 5
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
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) |
1.0.15
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  ) |
1.0.15
10 Jan 2022 15:15:39
|
Stefan Eßer (se) |
Fix CONFLICTS entries of multiple ports
There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.
This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.
Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port (Only the first 15 lines of the commit message are shown above ) |
1.0.15
20 Oct 2021 19:43:38
|
Jason W. Bacon (jwb) |
biology/bamutil: Update to 1.0.15
Numerous bug fixes and enhancements
Changes: https://github.com/statgen/bamUtil/releases/tag/v1.0.15 |
1.0.14
12 Oct 2021 16:40:35
|
Jason W. Bacon (jwb) |
biology/bamutil: Utilities for working with SAM/BAM files
Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health. It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc. |
Number of commits found: 5
|
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