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Port details
htslib C library for high-throughput sequencing data formats
1.17_1 biology on this many watch lists=1 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 1.17_1Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2014-12-14 22:35:26
Last Update: 2024-01-27 12:37:30
Commit Hash: 2eb9c98
People watching this port, also watch:: cytoscape, openjdk8, tmux, xen-kernel, python311
Also Listed In: devel
License: BSD3CLAUSE MIT
WWW:
https://www.htslib.org/
Description:
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.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (51 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/htslib-1.17_1/catalog.mk
  3. /usr/local/share/licenses/htslib-1.17_1/LICENSE
  4. /usr/local/share/licenses/htslib-1.17_1/BSD3CLAUSE
  5. /usr/local/share/licenses/htslib-1.17_1/MIT
  6. bin/bgzip
  7. bin/htsfile
  8. bin/tabix
  9. include/htslib/bgzf.h
  10. include/htslib/cram.h
  11. include/htslib/faidx.h
  12. include/htslib/hfile.h
  13. include/htslib/hts.h
  14. include/htslib/hts_defs.h
  15. include/htslib/hts_endian.h
  16. include/htslib/hts_expr.h
  17. include/htslib/hts_log.h
  18. include/htslib/hts_os.h
  19. include/htslib/kbitset.h
  20. include/htslib/kfunc.h
  21. include/htslib/khash.h
  22. include/htslib/khash_str2int.h
  23. include/htslib/klist.h
  24. include/htslib/knetfile.h
  25. include/htslib/kroundup.h
  26. include/htslib/kseq.h
  27. include/htslib/ksort.h
  28. include/htslib/kstring.h
  29. include/htslib/regidx.h
  30. include/htslib/sam.h
  31. include/htslib/synced_bcf_reader.h
  32. include/htslib/tbx.h
  33. include/htslib/thread_pool.h
  34. include/htslib/vcf.h
  35. include/htslib/vcf_sweep.h
  36. include/htslib/vcfutils.h
  37. lib/libhts.a
  38. lib/libhts.so
  39. lib/libhts.so.1.17
  40. lib/libhts.so.3
  41. libdata/pkgconfig/htslib.pc
  42. share/man/man1/bgzip.1.gz
  43. share/man/man1/htsfile.1.gz
  44. share/man/man1/tabix.1.gz
  45. share/man/man5/faidx.5.gz
  46. share/man/man5/sam.5.gz
  47. share/man/man5/vcf.5.gz
  48. share/man/man7/htslib-s3-plugin.7.gz
  49. @owner
  50. @group
  51. @mode
Collapse this list.
Dependency lines:
  • htslib>0:biology/htslib
To install the port:
cd /usr/ports/biology/htslib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/htslib
  • pkg install htslib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: htslib
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1677245487 SHA256 (htslib-1.17.tar.bz2) = 763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f SIZE (htslib-1.17.tar.bz2) = 4619884

Packages (timestamps in pop-ups are UTC):
htslib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.17_11.17_11.11.01.17_11.17_1-1.11.0-
FreeBSD:13:quarterly1.17_11.17_11.171.17_11.17_11.171.171.17
FreeBSD:14:latest1.17_11.17_11.161.17_11.17_11.17-1.17
FreeBSD:14:quarterly1.17_11.17_1-1.17_11.17_11.171.171.17
FreeBSD:15:latest1.17_11.17_1n/a1.17_1n/a1.17_11.17_11.17_1
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. autoconf>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
Test dependencies:
  1. bash : shells/bash
  2. perl5>=5.36<5.37 : lang/perl5.36
Library dependencies:
  1. libdeflate.so : archivers/libdeflate
  2. libcurl.so : ftp/curl
This port is required by:
for Libraries
  1. biology/augustus
  2. biology/bcf-score
  3. biology/bcftools
  4. biology/bio-mocha
  5. biology/cufflinks
  6. biology/freebayes
  7. biology/jellyfish
Expand this list (17 items / 10 hidden - sorry, this count includes any deleted ports)
  1. Collapse this list).
  2. biology/kallisto
  3. biology/mashmap
  4. biology/pbbam
  5. biology/py-pysam
  6. biology/samtools
  7. biology/star
  8. biology/tabixpp
  9. biology/vcflib
  10. biology/vt
  11. Collapse this list.

Deleted ports which required this port:

Expand this list of 1 deleted port
  1. biology/unanimity*
  2. Collapse this list of deleted ports.
* - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...

Configuration Options:
===> The following configuration options are available for htslib-1.17_1: CURL=on: Use libcurl for network file access (HTTPS and S3 support). ===> Use 'make config' to modify these settings
Options name:
biology_htslib
USES:
autoreconf cpe gmake localbase pathfix perl5 shebangfix tar:bzip2 ssl
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://github.com/samtools/htslib/releases/download/1.17/
Collapse this list.

Number of commits found: 26

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.17_1
27 Jan 2024 12:37:30
commit hash: 2eb9c98180f04a69241536e169b277747f1c46c6commit hash: 2eb9c98180f04a69241536e169b277747f1c46c6commit hash: 2eb9c98180f04a69241536e169b277747f1c46c6commit hash: 2eb9c98180f04a69241536e169b277747f1c46c6 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/htslib: Moved man to share/man

Approved by:    portmgr (blanket)
1.17
18 Apr 2023 21:55:29
commit hash: bba4910f8cf9cb77e587343c7fc81c5341ae52f9commit hash: bba4910f8cf9cb77e587343c7fc81c5341ae52f9commit hash: bba4910f8cf9cb77e587343c7fc81c5341ae52f9commit hash: bba4910f8cf9cb77e587343c7fc81c5341ae52f9 files touched by this commit
Robert Clausecker (fuz) search for other commits by this committer
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)
1.17
24 Feb 2023 23:23:25
commit hash: 5ce41514802cd442c01388c30a97e1fde16d836fcommit hash: 5ce41514802cd442c01388c30a97e1fde16d836fcommit hash: 5ce41514802cd442c01388c30a97e1fde16d836fcommit hash: 5ce41514802cd442c01388c30a97e1fde16d836f files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/htslib: Update to 1.17

Numerous enhancements and fixes

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

Reported by:    portscout
1.16
05 Jan 2023 23:16:08
commit hash: 2d9e290314480b09d4eb7340a10730c71e10a6b2commit hash: 2d9e290314480b09d4eb7340a10730c71e10a6b2commit hash: 2d9e290314480b09d4eb7340a10730c71e10a6b2commit hash: 2d9e290314480b09d4eb7340a10730c71e10a6b2 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/htslib: Update to 1.16

Numerous minor enhancements and bug fixes

Changes: https://github.com/samtools/htslib/releases
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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)
1.15
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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 View all of this commit message)
1.15
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
1.15
26 Feb 2022 15:04:10
commit hash: b3b13f54dcecb24ecd50e63fbdfdd32711a1b34ccommit hash: b3b13f54dcecb24ecd50e63fbdfdd32711a1b34ccommit hash: b3b13f54dcecb24ecd50e63fbdfdd32711a1b34ccommit hash: b3b13f54dcecb24ecd50e63fbdfdd32711a1b34c files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/htslib: Update to 1.15

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

Reported by:    portscout
1.14
18 Dec 2021 17:56:50
commit hash: 134a1c9046c43338aa898af4bb1ab257a5c0618bcommit hash: 134a1c9046c43338aa898af4bb1ab257a5c0618bcommit hash: 134a1c9046c43338aa898af4bb1ab257a5c0618bcommit hash: 134a1c9046c43338aa898af4bb1ab257a5c0618b files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/htslib: Update to 1.14

Several minor enhancements and fixes

Changes: https://github.com/samtools/htslib/tags
1.13
10 Sep 2021 21:18:20
commit hash: 8522c8336e1656c2058fb4052f10d945cf88f9f5commit hash: 8522c8336e1656c2058fb4052f10d945cf88f9f5commit hash: 8522c8336e1656c2058fb4052f10d945cf88f9f5commit hash: 8522c8336e1656c2058fb4052f10d945cf88f9f5 files touched by this commit
Bernhard Froehlich (decke) search for other commits by this committer
biology/htslib: Add CPE information

Approved by:	portmgr (blanket)
1.13
12 Jul 2021 13:16:45
commit hash: 5fa07128ec66ff71ca0348a324e2777eb00ee89acommit hash: 5fa07128ec66ff71ca0348a324e2777eb00ee89acommit hash: 5fa07128ec66ff71ca0348a324e2777eb00ee89acommit hash: 5fa07128ec66ff71ca0348a324e2777eb00ee89a files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
htslib: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/htslib/releases/tag/1.13
1.12
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
1.12
20 Mar 2021 17:14:32
Revision:568874Original commit files touched by this commit
jwb search for other commits by this committer
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
1.11.0
05 Nov 2020 20:30:50
Revision:554155Original commit files touched by this commit
jwb search for other commits by this committer
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
1.10.2
03 Aug 2020 17:40:04
Revision:544090Original commit files touched by this commit
jwb search for other commits by this committer
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
1.9
02 Aug 2018 19:27:13
Revision:476245Original commit files touched by this commit
fernape search for other commits by this committer
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
1.8
16 Jul 2018 18:11:44
Revision:474752Original commit files touched by this commit
yuri search for other commits by this committer
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)
1.6
25 Oct 2017 10:19:50
Revision:452840Original commit files touched by this commit
pizzamig search for other commits by this committer
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
1.3.1
21 Oct 2016 15:21:13
Revision:424427Original commit files touched by this commit
mat search for other commits by this committer
Use USES=pathfix where applicable.

PR:		213195
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
Differential Revision:	https://reviews.freebsd.org/D8093
1.3.1
26 May 2016 20:28:55
Revision:415914Original commit files touched by this commit
pi search for other commits by this committer
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)
1.3
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
1.3
29 Dec 2015 15:05:44
Revision:404749Original commit files touched by this commit
marino search for other commits by this committer
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.
1.3
25 Dec 2015 01:31:09
Revision:404398Original commit files touched by this commit
junovitch search for other commits by this committer
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)
1.2.1
06 May 2015 15:16:54
Revision:385521Original commit files touched by this commit
mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
1.2.1
06 Mar 2015 12:45:23
Revision:380596Original commit files touched by this commit
robak search for other commits by this committer
biology/htslib: update 1.1 -> 1.2.1

PR:		198291
Submitted by:	Reed Cartwright <cartwright@asu.edu>
1.1
14 Dec 2014 22:35:08
Revision:374729Original commit files touched by this commit
pawel search for other commits by this committer
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>

Number of commits found: 26