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Port details
bamutil Utilities for working with SAM/BAM files
1.0.15 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 1.0.15Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-10-12 16:45:03
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (4 items)
Collapse this list.
  1. bin/bam
  2. /usr/local/share/licenses/bamutil-1.0.15/catalog.mk
  3. /usr/local/share/licenses/bamutil-1.0.15/LICENSE
  4. /usr/local/share/licenses/bamutil-1.0.15/GPLv3
Collapse this list.
Dependency lines:
  • bamutil>0:biology/bamutil
Conflicts:
CONFLICTS_INSTALL:
  • bam
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
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

Expand this list (2 items)

Collapse this list.

SHA256 (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 075dcd891409c48d76c0c66186c0cc479bc3cd50bba093e7f318e1d1d19961ff SIZE (statgen-libStatGen-v1.0.15_GH0.tar.gz) = 560782

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Packages (timestamps in pop-ups are UTC):
bamutil
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.0.151.0.15-1.0.151.0.15---
FreeBSD:13:quarterly1.0.151.0.151.0.151.0.151.0.151.0.151.0.151.0.15
FreeBSD:14:latest1.0.151.0.151.0.151.0.151.0.151.0.15-1.0.15
FreeBSD:14:quarterly1.0.151.0.15-1.0.151.0.151.0.151.0.151.0.15
FreeBSD:15:latest1.0.151.0.15n/a1.0.15n/a1.0.151.0.151.0.15
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
This port is required by:
for Run
  1. 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:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/statgen/bamUtil/tar.gz/v1.0.15?dummy=/
Collapse this list.

Number of commits found: 5

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
1.0.15
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)
1.0.15
10 Jan 2022 15:15:39
commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash: bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
1.0.15
20 Oct 2021 19:43:38
commit hash: 9636d7ad40ffca979ea17d6e6033c1a5ae430ae4commit hash: 9636d7ad40ffca979ea17d6e6033c1a5ae430ae4commit hash: 9636d7ad40ffca979ea17d6e6033c1a5ae430ae4commit hash: 9636d7ad40ffca979ea17d6e6033c1a5ae430ae4 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2commit hash: cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2commit hash: cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2commit hash: cdf2ff2f68e6d4e78f85124aa5fbd8371adaebc2 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
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