Trimadap is a small tool to trim adapter sequences from Illumina data. It
performs SSE2-SW between each read and each adapter sequence and identifies
adapter sequences with a few heuristic rules which can be found in the
ta_trim1() function in trimadap-mt.c. The default adapters it uses are included
in illumina.txt. These are typical Illumina adapters from paired-end
sequencing.
Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing
any more scientific computing support in the future. I have continued
to maintain ~160 ports to the best of my ability, mainly as a favor to
the community, but I can no longer justify the time and effort
required. I am therefore releasing most of my scientific ports, along
with a few others, to ports@. I will continue to maintain ports I am
actively using and those for which I am upstream.
biology/trimadap: Update to 0.1.4
Update to latest commit, with new MIT license
Add support for other architectures using SIMDE
Reported by: fuz
Reviewed by: fuz
Differential Revision: https://reviews.freebsd.org/D47129
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)
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 )
Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)
ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should
start with lower-case letter and not end with a period which is added
by the framework, similar to other knobs like BROKEN, IGNORE, et al.
While here, remove needless quoting, add missing Oxford comma, expand
contractions and jargonisms, use correct spelling for proper names.
biology/trimadap: Trim adapter sequences from Illumina data
Reviewed by: mat
Approved by: jrm
Differential Revision: https://reviews.freebsd.org/D14935
