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.
===> The following configuration options are available for htslib-1.24_1:
CURL=on: Use libcurl for network file access (HTTPS and S3 support).
PLUGINS=on: Build and/or install plugins
===> Use 'make config' to modify these settings
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: 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: 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)
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.
(Only the first 15 lines of the commit message are shown above )
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>
(Only the first 15 lines of the commit message are shown above )
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 1.10.2
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
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: 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)
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>
