biology/minimap22.31

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/minimap2: Update to 2.31

A few bug fixes and enhancements
New subcommands sim2bed and badread2fa
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout

all: drop support for FreeBSD 13, mips and risc64sf

Reviewed by:            many (*)
Differential Revision:  https://reviews.freebsd.org/D55624
Differential Revision:  https://reviews.freebsd.org/D55642 (merged in from bofh)

many (*)
  acm arrowd brooks cmt dch decke dinoex eduardo fluffy fuz gahr garga
  jbeich joerg jrm kai kenrap martymac matthew mfechner michaelo mizhka
  nobutaka pkubaj se tagattie thj

  Anton Saietskii
  GenericRikka
  Gert Doering
  Jan Bramkamp
  Oleh Hushchenkov
  Oleksandr Kryvulia
  Ralf van der Enden
  Yamagi

  desktop kde python tcltk office

biology/minimap2: Remove extraneous file that snuck in the last commit

biology/minimap2: Update to 2.30

Deprecate several subcommands, replaced by minigff
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout

biology/minimap2: Update to 2.29

A few new features and fixes
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout

biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors

Upstream supports specific architectures, mainly 64-bit and ARM Neon

biology/minimap2: Unbreak build on aarch64

Remove unsupports -msse flags

Reported by:    pkg-fallout

biology/minimap2: Fix man prefix

Missed in last update, done just before prefix/man was obsoleted

biology/minimap2: Update to 2.28

Fix --MD flag
Add experimental lr:hqae
Changes: https://github.com/lh3/minimap2/releases

Reported by:    portscout

biology/minimap2: Move man page to share/man

Approved by:	portmgr (blanket)

biology/minimap2: Update to 2.27

Several new features and a few bug fixes
Changes: https://github.com/lh3/minimap2/releases

Reported by: portscout

biology/minimap2: Move man pages to share/man

Approved by:	portmgr (blanket)

biology/minimap2: Update to 2.25

New feature to output sequences in secondary alignments
Several minor enhancements and fixes
Changes: https://github.com/lh3/minimap2/releases

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/minimap2: Update to 2.24

Fix chaining algorithm issue resulting in poorly aligned regions

Reported by:    portscout

biology/minimap2: Unbreak on i386 by resotring -msse flags

biology/minimap2: Update to 2.23

Also switch to SIMDE Makefile to support non-x86 platforms

Changes:        https://github.com/lh3/minimap2/releases/tag/v2.23
Reported 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/minimap2: Add pkg-plist to repo

biology/minimap2: Update to 2.22

Changelog: https://github.com/lh3/minimap2/releases/tag/v2.22

Reported by:    portscout

biology/minimap2: Update to 2.20

Add "extra" binaries to install

Changes:    https://github.com/lh3/minimap2/releases/tag/v2.20

biology/minimap2: Update to 2.18

Numerous bug fixes and a few minor improvements

Reported by:    portscout

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

Remove # $FreeBSD$ from Makefiles.

biology/minimap2: Upgrade to 2.17

Reported by:    portscout

biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.