biology/htslib1.24_1

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/htslib: Remove obsolete patches

Patches for aarch64 were erroneously restored due to a transient
build failure on my M1, which was misinterpreted.

biology/htslib: Update to 1.24

Numerous fixes and enhancements
Changes: https://github.com/samtools/htslib/releases

Reported by:    portscout

biology/htslib: fix build on armv7 (again)

The patches provided by me in 2023 to fix the build on armv7 were
upstreamed shortly after.  In a subsequent update to the port, it
appears that the maintainer had then reversed these patches (?!),
effectively undoing my now upstreamed bug fix.

Remove the bogus patches to fix the build.

Fixes:		aafe5d31c5f3afdaad0f6345bee06e7a3e2c5ced
See also:	https://github.com/samtools/htscodecs/issues/81
Approved by:	portmgr (build fix blanket)
MFH:		2026Q2

biology/htslib: Update to 1.23.1

Numerous bug fixes
Changes: https://github.com/samtools/htslib/releases
Added PLUGINS option to build with external plugins enabled

biology/*: remove useless USES=pathfix

biology/htslib: Update to 1.22

Numerous fixes and enhancements
Changes: https://github.com/samtools/htslib/releases
Updated by: Hayzam Sherif
Tested all dependent ports, no breaking API/ABI changes

Reported by:    portscout

biology/htslib: Update to 1.21

Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/htslib/releases

Reported by:    portscout

biology/htslib: Moved man to share/man

Approved by:    portmgr (blanket)

biology/htslib: fix build on armv7

This project includes some SIMD-enhanced functions for ARM NEON.
Unfortunately the code uses a bunch of intrinsics only available on
aarch64.  Disable the use of NEON on armv6 and armv7 to fix the build
on these platforms.

See also:	https://github.com/samtools/htslib/issues/1603
Approved by:	portmgr (build fix blanket)

biology/htslib: Update to 1.17

Numerous enhancements and fixes

Changes:    https://github.com/samtools/htslib/releases

Reported by:    portscout

biology/htslib: Update to 1.16

Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/htslib/releases

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: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr

biology/htslib: Update to 1.15

A few minor bug fixes and enhancements
No API changes affecting existing dependents

Reported by:    portscout

biology/htslib: Update to 1.14

Several minor enhancements and fixes

Changes: https://github.com/samtools/htslib/tags

biology/htslib: Add CPE information

Approved by:	portmgr (blanket)

htslib: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/htslib/releases/tag/1.13

Remove # $FreeBSD$ from Makefiles.

biology/htslib: Update to 1.12 biology/samtools: Update to 1.12 biology/bcftools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.11

Build-tested all other htslib dependents, no revbumps should be needed

Reported by:    portscout

biology/htslib: Upgrade to 1.11.0

Numerous bug fixes, new features and performance improvements since 1.10
https://github.com/samtools/htslib/releases/tag/1.11

Reported by:    portscout

biology/htslib: Upgrade to 1.10.2

Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags

Bump PORTREVISION on dependents that don't require additional patching

PR:             248089

biology/htslib: update to 1.9

PR:	230170
Submitted by:	ndowens.fbsd@yandex.com
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D16568

biology/htslib: Update 1.6 -> 1.8

Port changes:
* Use DISTVERSION
* Add USES=localbase instead of CPPFLAGS/LDFLAGS
* Move USES=ssl to CURL_USES=ssl
* Update WWW

PR:		228908
Approved by:	maintainer's timeout (cartwright@asu.edu; 35 days)

biology/htslib biology/bcftools biology/samtools: Update to 1.6

PR:		223094
Submitted by:	mzaki@niid.go.jp
Approved by:	cartwright@asu.edu (maintainer)
Approved by:	olivier (mentor)
Differential Revision:	https://reviews.freebsd.org/D12768

Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093

biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1

Changes:
  https://sourceforge.net/p/samtools/mailman/message/35033807/

PR:		209653
Submitted by:	cartwright@asu.edu (maintainer)

Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight

biology/htslib: Replace FreeBSD-specific fix with a generic one

This port will not build if ENOTRECOVERABLE is not defined, period.
It's not necessary to check OPSYS and version, just apply the fallback
definition if it's not defined.  This unbreaks DragonFly after last
commit.

biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3

- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
  version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's

PR:		205524
PR:		205525
PR:		205526
Submitted by:	cartwright@asu.edu (maintainer)

Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight

biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>

HTSlib is an implementation of a unified C library for accessing common file formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing data. It is the core library used by samtools and bcftools.

WWW: http://www.htslib.org/

PR:		195591
Submitted by:	Reed A. Cartwright <cartwright@asu.edu>