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.

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>

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>