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Port details
sam2pairwise Show pairwise alignment for each read in a SAM file
1.0.0 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 1.0.0Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-09-07 20:36:08
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: MIT
WWW:
https://github.com/mlafave/sam2pairwise
Description:
sam2pairwise takes a SAM file and uses the CIGAR and MD tag to reconstruct the pairwise alignment of each read.
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/sam2pairwise
  2. /usr/local/share/licenses/sam2pairwise-1.0.0/catalog.mk
  3. /usr/local/share/licenses/sam2pairwise-1.0.0/LICENSE
  4. /usr/local/share/licenses/sam2pairwise-1.0.0/MIT
Collapse this list.
Dependency lines:
  • sam2pairwise>0:biology/sam2pairwise
To install the port:
cd /usr/ports/biology/sam2pairwise/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/sam2pairwise
  • pkg install sam2pairwise
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: sam2pairwise
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1631041315 SHA256 (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 899d3db071cc248870bbedbdb39784de4c54c9a7888bc408022e809ace47ec0e SIZE (mlafave-sam2pairwise-v1.0.0_GH0.tar.gz) = 10013

Packages (timestamps in pop-ups are UTC):
sam2pairwise
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.0.01.0.0-1.0.01.0.0---
FreeBSD:13:quarterly1.0.01.0.01.0.01.0.01.0.01.0.01.0.01.0.0
FreeBSD:14:latest1.0.01.0.01.0.01.0.01.0.01.0.0-1.0.0
FreeBSD:14:quarterly1.0.01.0.0-1.0.01.0.01.0.01.0.01.0.0
FreeBSD:15:latest1.0.01.0.0n/a1.0.0n/a1.0.01.0.01.0.0
This port has no dependencies.
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
No options to configure
Options name:
biology_sam2pairwise
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/mlafave/sam2pairwise/tar.gz/v1.0.0?dummy=/
Collapse this list.

Number of commits found: 3

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)
1.0.0
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)
1.0.0
07 Sep 2021 20:32:29
commit hash: e61df5e464758cb1d460c95b4fbb3855a4f7f6dccommit hash: e61df5e464758cb1d460c95b4fbb3855a4f7f6dccommit hash: e61df5e464758cb1d460c95b4fbb3855a4f7f6dccommit hash: e61df5e464758cb1d460c95b4fbb3855a4f7f6dc files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
reconstruct the pairwise alignment of each read.

Number of commits found: 3