biology/vsearch2.32.0

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/vsearch: Update to 2.32.0

Numererous bug fixes, new per-command man pages, and a few other
enhancements.
Changes: https://github.com/torognes/vsearch/releases
Normally I don't upgrade ports so close to the end of a quarter, but
this release has a lot of bug fixes, which I think outweigh the risk
of a regression slipping into the next quarterly branch.

Reported by:    portscout

biology/vsearch: Update to 2.31.0

Numerous bug fixes and a few enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.6

Fix regression introduced in 2.30.1
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.5

A few fixes and minor improvements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.4

Fix incorrect scores reported for some non-chimeric sequences
during chimera detection.
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.3

Fix memory allocation bug
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Add patch for FreeBSD 16

Resolve collision with symbol "memalignment"

Reported by:    pkg-fallout

biology/vsearch: Update to 2.30.2

Allow a UDB file to be written to a pipe or stdout
Correct computation of median cluster size after dereplication
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.1

Numerous small fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.30.0

Add options --n_mismatch, --fastq_minqual, and --fastq_truncee_rate
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.29.4

Fix regression from 2.23.0 regarding chimera detection
Add pragma to ensure correct code
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.29.2

Fix seg fault when cluster set is empty
Reported by:    portscout

biology/vsearch: Update to 2.29.1

Fix a seg fault in 2.29.0

Reported by:    portscout

biology/vsearch: Update to 2.29.0

Several bug fixes
Support for RISC-V
Improved testing
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.28.1

A few bug fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.27.1

Fix weak_id option and make searches report weak hits in some cases
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Move man pages to share/man

Approved by:	portmgr (blanket)

biology/vsearch: Update to 2.27.0

Add FASTQ support to usearch_global and search_exact
Code cleanup and manual clarifications

Reported by:    portscout

biology/vsearch: Update to 2.26.1

A few minor enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.25.0

chimeras_denovo: Allow user to specify mismatch tolerance

Changes: https://github.com/torognes/vsearch/releases

*/*: Bump PORTREVISION for Ghostscript 10 change

Reported by:	sunpoet
Approved by:	jrm (mentor), sunpoet
Differential Revision:	https://reviews.freebsd.org/D42412

biology/vsearch: Update to 2.24.0

Upstream code cleanup
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.23.0

Numerous minor fixes and enhancements
Changes: https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.22.1

Add the derep_smallmem command for dereplication with less memory usage
Changes:    https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.21.2

Fix problems with the --lcaout option
Changes:        https://github.com/torognes/vsearch/tags

Reported by:    portscout

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.

This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.

There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.

The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.

Approved by:		portmgr (tcberner)

biology/vsearch: Update to 2.21.1

Adds the sample, qsegout and tsegout options. It also enables the use of
UDB databases with uchime_ref.

Changes:        https://github.com/torognes/vsearch/releases

Reported by:    portscout

biology/vsearch: Update to 2.19.0

A few bug fixes, new subcommands and options

Changes:        https://github.com/torognes/vsearch/tags
Reporte by:     portscout

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/vsearch: Update to 2.17.1

Changes:    https://github.com/torognes/vsearch/releases

Also enabled powerpc64le

biology/vsearch: Update to 2.17.0

Afterthoughts from the recent 2.16.0 release
(Minor bug fixes and enhancements to the new orient subcommand)

Reported by:    portscout

One more small cleanup, forgotten yesterday. Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/vsearch: Update to 2.16.0

Add "orient" subcommand
A few other fixes and enhancements

Reported by:    portscout

biology/vsearch: Update to 2.15.2

Code clean up and modernization

Reported by:    portscout

biology/vsearch: enable on powerpc64le

biology/vsearch: Update to 2.15.0

Numerous minor enhancements

biology/vsearch: Upgrade to 2.14.2

Numerous small bug fixes and enhancements

Reported by:    portscout

biology/vsearch: Update to 2.13.4

FreeBSD patches incorporated into new upstream release

Reported by:    portscout

biology/vsearch: Remove powerpc64 support

Requires little endian mode and FreeBSD currently does not support it

biology/vsearch: Versatile open-source tool for metagenomics

VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.

The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).