biology/bwa0.7.19

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

*/*: Älven's ports to use FreeBSD.org email

PR:		288046
Approved by:	mentors db@, yuri@ (implicit)

biology/bwa: update 0.7.18 => 0.7.19

ChangeLog:
https://github.com/lh3/bwa/blob/master/NEWS.md#release-0719-22-march-2025

Notable changes:

 * Bugfix: internal @HD lines. The bug was introduced in 0.7.18.
 * Merged #414, #391, #346, #312, #311, #308, #291, #288, #286 and #212

PR:		285620
Reported by:	alster@vinterdalen.se (maintainer)

biology/bwa: small improvements

Add supplementary WWWs.
Remove unneeded USES=tar:bzip2. Upstream uses common tar.gz archives.

PR:		283873
Approved by:	submitter is maintainer

bwa: New maintainer

biology/bwa: Update to 0.7.18

Official support for aarch64 (we already had this patched in)
A few minor enhancements and fixes
Changes: https://github.com/lh3/bwa/releases

PR:             282923
Reported by:    alster@vinterdalen.se

MAN?PREFIX: eleminate its usage  and move man to share/man

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/bwa: don't use GCC on powerpc64le

Now that the port uses simde, it builds fine without gcc's translation.

biology/bwa: Unbreak on most non-x86 platforms using simde

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

Remove # $FreeBSD$ from Makefiles.

biology/bwa: fix build on powerpc64le

Use GCC's SSE->Altivec translation:
In file included from ksw.c:29:
In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13:
In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13:
/usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size
    return (__m64)__builtin_ia32_vec_init_v2si(__i, 0);

For ports on riscv64 that fail the same (or similar ways) to aarch64, mark them BROKEN.

While here, pet portlint (Makevar order).

Approved by:	portmgr (tier-2 blanket)

biology/bwa: fix build on recent current

Obtained from:	https://github.com/lh3/bwa/commit/2a1ae7b6f34a96ea25be007ac9d91e57e9d32284

Multiple ports: Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128

[unbreak] biology/bwa: Remove old patch files

Approved by: jrm
Differential Revision:  https://reviews.freebsd.org/D13314

For ports that are marked BROKEN on armv6, and also fail to build on armv7, mark them so.

This is part two of a multipart commit to bring armv7 ports to parity
with armv6.

Approved by:	portmgr (tier-2 blanket)
Obtained from:	lonesome.com -exp run

biology/bwa: Upgrade to 0.7.17

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13283

Mark some ports failing on armv6, for errors classified as "???".

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Mark some ports failing on power64.  In cases where the error message was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)

Mark various ports broken on aarch64 and armv6.

Approved by:	portmgr (tier-2 blanket)

Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/

Attempt to fix build on non-x86 archs.

Approved by:	portmgr (tier-2 blanket)

mark some of the ports that don't build on powerpc64 for me

- Update maintainer mail address - Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493

BWA is a program for aligning sequencing reads against a large reference genome (e.g. human genome). It has two major components, one for read shorter than 150bp and the other for longer reads.

WWW: http://sourceforge.net/projects/bio-bwa/

PR:		203158
Submitted by:	Jason Bacon <jwbacon@tds.net>