14:53 Jason W. Bacon (jwb) 

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

    57d280a

21:10 Stefan Eßer (se) 

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)

    b7f0544

14:30 Jason W. Bacon (jwb) 

biology/minimap2: Update to 2.24

Fix chaining algorithm issue resulting in poorly aligned regions

Reported by:    portscout

    2b4cfc8

17:22 Jason W. Bacon (jwb) 

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

    8261e82

16:29 Jason W. Bacon (jwb) 

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

    325754d

12:58 Alexey Dokuchaev (danfe) 

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.

    61b6613

14:15 Jason W. Bacon (jwb) 

biology/minimap2: Update to 2.22

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

Reported by:    portscout

    205fcac

21:06 Jason W. Bacon (jwb) 

biology/minimap2: Update to 2.20

Add "extra" binaries to install

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

    da0bb00

19:18 Jason W. Bacon (jwb) 

biology/minimap2: Update to 2.18

Numerous bug fixes and a few minor improvements

Reported by:    portscout

    a2fa050

08:09 Mathieu Arnold (mat) 

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

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

14:56 jwb 

biology/minimap2: Upgrade to 2.17

Reported by:    portscout

 

18:03 jwb 

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.