brew

Installer htslib avec Homebrew, dnf, MacPorts, Nix, apt, zypper

Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de htslib pour les workflows d'agents IA.

Commande d'installation Notes de sécurité

installation

Commandes d'installation supplémentaires

macOS

Homebrewvérifié · 100%

brew install htslib

local Homebrew formula metadata

MacPortsvérifié · 94%

sudo port install htslib

MacPorts ports tree · science/htslib/Portfile · Source: api.github.com

Linux

Fedora dnfvérifié · 92%

sudo dnf install htslib

Fedora Rawhide package metadata · htslib · Source: dl.fedoraproject.org

Nixvérifié · 92%

nix profile install nixpkgs#htslib

nixpkgs package indexes · pkgs/by-name/ht/htslib/package.nix · Source: api.github.com

Debian aptvérifié · 92%

sudo apt install htslib-test

Debian stable package indexes · htslib-test · Source: deb.debian.org

openSUSE zyppervérifié · 92%

sudo zypper install bgzip

openSUSE Tumbleweed package metadata · bgzip · Source: download.opensuse.org

aperçu

Résumé du paquet

C library for high-throughput sequencing data formats

Liens du projet

Commandes et alias

annot-tsv
bgzip
htsfile
ref-cache
tabix

historique

Historique du projet et usages

HTSlib is the C library layer of the Samtools family, providing shared reading and writing support for high-throughput sequencing formats such as SAM, BAM, CRAM, VCF, and BCF. It matters beyond a single command-line package because many genomics tools build on the same file-format and indexing behavior.

Historique du projet

The Samtools site describes the project as three related repositories: Samtools for alignment manipulation, BCFtools for variant data, and HTSlib as the common C library. Its download page preserves the split in historical context, noting that before HTSlib was introduced, Samtools and BCFtools were shipped together in a single samtools-0.1.x source package.

The annotated 1.0 tag in the official GitHub repository, dated 2014-08-15, describes the first HTSlib release as supporting SAM, BAM, CRAM, VCF, and BCF. Later release notes show the library continuing to absorb format, indexing, threading, remote-I/O, and ABI changes that affect downstream tools.

Historique d'adoption

HTSlib's adoption is tightly coupled to the Samtools ecosystem: the Samtools site says Samtools and BCFtools use HTSlib internally, while HTSlib is also distributed separately for developers writing programs against its API. Packaging across Homebrew, Debian-family distributions, Fedora, MacPorts, Nix, and openSUSE reflects its role as a build-time and runtime dependency rather than only an end-user utility.

Modes d'utilisation

Package users often encounter HTSlib through utilities installed with the library, especially bgzip, htsfile, tabix, ref-cache, and annot-tsv. Developers use the C API for compressed genomic files, indexes, region queries, remote access, and format detection in sequencing and variant-analysis workflows.

Pourquoi les passionnés de paquets s'y intéressent

HTSlib is package-nerd significant because it is both a library ABI and a bundle of small Unix-style genomics tools. Changes such as the 2019 1.10 release's SAM header API, multi-threaded SAM I/O, on-the-fly indexing, S3 updates, and 64-bit reference-position support are the sort of low-level package events that can ripple through many bioinformatics builds.

Chronologie

2012: The samtools/htslib repository was created on GitHub.
2014: The 1.0 tag marked the first HTSlib release, supporting SAM, BAM, CRAM, VCF, and BCF.
2019: Release 1.10 added a SAM header API, multi-threaded SAM reading and writing, on-the-fly indexing, and S3 interface updates.
2026: Release notes for 1.23.1 documented CRAM decoder security fixes and related build updates.

Related projects

Samtools and BCFtools are the closest sibling projects, both using HTSlib internally. Related file-format work includes the SAM, BAM, CRAM, VCF, BCF, BGZF, and tabix indexing formats that HTSlib reads, writes, or helps index.

Sources

Samtools project site, HTSlib download notes, GitHub repository metadata, and official release/tag metadata.

posture de sécurité

Niveau de risque : vert

library-like package without higher-risk signals.

Classificateur de risque

risque vert · confiance faible · appliance

Pourquoi

library-like package without higher-risk signals

Signaux

metadata:library-like

Comportement d'installation

Aucun hook post-install Homebrew n’est enregistré dans les métadonnées de formule.
Les métadonnées de bottle Homebrew sont disponibles pour 6 plateformes.
S’installe avec 2 dépendances d’exécution.

Revue recommandée

Avant une utilisation sans surveillance par un agent, vérifiez si l'outil lit des identifiants en clair, écrit un état distant, publie des artefacts ou lance des plugins.

exécutables

Exécutables installés

Commande	Type	Exposition
`annot-tsv`	cli	exécutable global
`bgzip`	cli	exécutable global
`htsfile`	cli	exécutable global
`ref-cache`	cli	exécutable global
`tabix`	cli	exécutable global

fraîcheur

Version et fraîcheur

Ces signaux séparent l'âge de génération de la page, l'activité du gestionnaire de paquets et la comparaison avec les versions amont. Un retard de version n'est signalé que lorsqu'une URL de preuve et des versions comparables sont présentes.

page générée2026-07-10

version du gestionnaire1.24

gestionnaire mis à jour2026-07-09

données localesOK

amontnot checked

dernière version détectéenon détecté

https://github.com/samtools/htslib

infoNo cached GitHub release or tag data was available.https://github.com/samtools/htslibconfiance none

métadonnées d'installation

Métadonnées du paquet

Clé du paquet	brew:htslib
Version	1.24
Gestionnaire de paquets	Homebrew
Page du gestionnaire de paquets	https://formulae.brew.sh/formula/htslib
Page d'accueil	https://www.htslib.org/
Dépôt	https://github.com/samtools/htslib
Docs amont	https://github.com/samtools/htslib#readme
Licence	MIT AND BSD-3-Clause
Archive source	https://github.com/samtools/htslib/releases/download/1.24/htslib-1.24.tar.bz2
Dernière mise à jour	2026-07-09T19:51:46Z
Pulse	updated
Dépendances	libdeflate, xz
Bibliothèques fournies par macOS	bzip2, curl
Bouteille	disponible (sur arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
post-install Homebrew	non défini
Service	aucun déclaré

faits du registre

Détails de la base source

Source Database	Homebrew formula API
Tap	homebrew/core
Full Name	htslib
Version Scheme	0
Revision	0
Bottle Stable Root URL	https://ghcr.io/v2/homebrew/core
Deprecated	no
Disabled	no
Keg Only	no
URL Keys	stable

correspondances dans les bases sources

Autres enregistrements de gestionnaires de paquets

Les correspondances proviennent d’index externes de gestionnaires de paquets et restent séparées des liens de paquets Automic Vault locaux.

Debian apt95%

htslib-test 1.21+ds-1

Test data for HTSlib

https://github.com/samtools/htslib

sudo apt install htslib-test

Section: libs
Architecture: all
Source Package: htslib
1 Dépendances
normalized package name match
Correspondance par : Htslib

Debian stable package indexes · deb.debian.org · Debian stable package indexes: htslib-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Debian apt95%

libhts-dev 1.21+ds-1

development files for the HTSlib

https://github.com/samtools/htslib

sudo apt install libhts-dev

Section: libdevel
Architecture: amd64
Source Package: htslib
6 Dépendances
normalized package name match
Correspondance par : Htslib

Debian stable package indexes · deb.debian.org · Debian stable package indexes: libhts-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Debian apt95%

libhts3t64 1.21+ds-1

C library for high-throughput sequencing data formats

https://github.com/samtools/htslib

sudo apt install libhts3t64

Section: libs
Architecture: amd64
Source Package: htslib
8 Dépendances
1 fournit
normalized package name match
Correspondance par : Htslib

Debian stable package indexes · deb.debian.org · Debian stable package indexes: libhts3t64 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Debian apt95%

tabix 1.21+ds-1

generic indexer for TAB-delimited genome position files

https://github.com/samtools/htslib

sudo apt install tabix

Section: science
Architecture: amd64
Source Package: htslib
6 Dépendances
normalized package name match
Correspondance par : Htslib

Debian stable package indexes · deb.debian.org · Debian stable package indexes: tabix from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz

Nix95%

htslib

nix profile install nixpkgs#htslib

normalized package name match
Correspondance par : Htslib

nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ht/htslib/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1

Ubuntu apt95%

htslib-test 1.19+ds-1.1build3

Test data for HTSlib

https://github.com/samtools/htslib

sudo apt install htslib-test

Section: universe/libs
Architecture: all
Source Package: htslib
1 Dépendances
normalized package name match
Correspondance par : Htslib

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: htslib-test from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

Ubuntu apt95%

libhts-dev 1.19+ds-1.1build3

development files for the HTSlib

https://github.com/samtools/htslib

sudo apt install libhts-dev

Section: universe/libdevel
Architecture: amd64
Source Package: htslib
5 Dépendances
normalized package name match
Correspondance par : Htslib

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libhts-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

Ubuntu apt95%

libhts3t64 1.19+ds-1.1build3

C library for high-throughput sequencing data formats

https://github.com/samtools/htslib

sudo apt install libhts3t64

Section: universe/libs
Architecture: amd64
Source Package: htslib
8 Dépendances
1 fournit
normalized package name match
Correspondance par : Htslib

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libhts3t64 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

Ubuntu apt95%

tabix 1.19+ds-1.1build3

generic indexer for TAB-delimited genome position files

https://github.com/samtools/htslib

sudo apt install tabix

Section: universe/science
Architecture: amd64
Source Package: htslib
6 Dépendances
normalized package name match
Correspondance par : Htslib

Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: tabix from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

dnf95%

htslib 1.23.1-2.fc45

C library for high-throughput sequencing data formats

http://www.htslib.org

sudo dnf install htslib

License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
Category: Unspecified
Architecture: i686
Source Package: htslib
8 Dépendances
2 fournit
normalized package name match
Correspondance par : Htslib

Fedora Rawhide package metadata · dl.fedoraproject.org · Fedora Rawhide package metadata: htslib from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst

dnf95%

htslib-devel 1.23.1-2.fc45

Development files for htslib

http://www.htslib.org

sudo dnf install htslib-devel

License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
Category: Unspecified
Architecture: i686
Source Package: htslib
3 Dépendances
2 fournit
normalized package name match
Correspondance par : Htslib

Fedora Rawhide package metadata · dl.fedoraproject.org · Fedora Rawhide package metadata: htslib-devel from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst

dnf95%

htslib-tools 1.23.1-2.fc45

Additional htslib-based tools

http://www.htslib.org

sudo dnf install htslib-tools

License: MIT AND BSD-3-Clause AND LicenseRef-Fedora-Public-Domain
Category: Unspecified
Architecture: x86_64
Source Package: htslib
8 Dépendances
1 fournit
normalized package name match
Correspondance par : Htslib

Fedora Rawhide package metadata · dl.fedoraproject.org · Fedora Rawhide package metadata: htslib-tools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst

MacPorts95%

htslib

sudo port install htslib

normalized package name match
Correspondance par : Htslib

MacPorts ports tree · api.github.com · MacPorts ports tree: science/htslib/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

zypper92%

bgzip 1.21-1.3

Block compression/decompression utility from the HTSlib project

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

sudo zypper install bgzip

License: MIT
Category: Productivity/Scientific/Other
Architecture: x86_64
Source Package: libhts
8 Dépendances
1 fournit
installed executable or alias match
Correspondance par : Bgzip

openSUSE Tumbleweed package metadata · download.opensuse.org · openSUSE Tumbleweed package metadata: bgzip from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst

zypper92%

htsfile 1.21-1.3

Identify high-throughput sequencing data files from the HTSlib project

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

sudo zypper install htsfile

License: MIT
Category: Productivity/Scientific/Other
Architecture: x86_64
Source Package: libhts
9 Dépendances
1 fournit
installed executable or alias match
Correspondance par : Htsfile

openSUSE Tumbleweed package metadata · download.opensuse.org · openSUSE Tumbleweed package metadata: htsfile from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst

zypper92%

tabix 1.21-1.3

Generic indexer for TAB-delimited genome position files from the HTSlib project

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

sudo zypper install tabix

License: MIT
Category: Productivity/Scientific/Other
Architecture: x86_64
Source Package: libhts
10 Dépendances
1 fournit
installed executable or alias match
Correspondance par : Tabix

openSUSE Tumbleweed package metadata · download.opensuse.org · openSUSE Tumbleweed package metadata: tabix from https://download.opensuse.org/tumbleweed/repo/oss/repodata/be8d3611d25469107f32075a1697e69ec57a2b850b42348a658cc671ad5ec2b50760d02c3e59524d50da9a11d5be799bdaffba2e166e8ca8858512e3c0bd665d-primary.xml.zst

piste source

Généré depuis les données du dépôt

Cette page est servie par av-web depuis l'artéfact SQLite privé des paquets généré par scripts/generate-pkg-sqlite.py.

Combined YAML source

View the package source record on GitHub.

combined/htslib.yml

Sources utilisées

Geiger risk classifier
Nucleus package database
av.db category and tag curation
cross-ecosystem install command graph
curated package history
external package-manager database matches
package relationship graph
package version freshness
package-page enrichment

Installer htslib avec Homebrew, dnf, MacPorts, Nix, apt, zypper

Commandes d'installation supplémentaires

macOS

Linux

Résumé du paquet

Liens du projet

Commandes et alias

Historique du projet et usages

Historique du projet

Historique d'adoption

Modes d'utilisation

Pourquoi les passionnés de paquets s'y intéressent

Chronologie

Related projects

Sources

Niveau de risque : vert

Classificateur de risque

Pourquoi

Signaux

Comportement d'installation

Revue recommandée

Exécutables installés

Version et fraîcheur

Métadonnées du paquet

Détails de la base source

Autres enregistrements de gestionnaires de paquets

Liens internes de paquets

Hubs thématiques

Outils liés

Même workflow

Guides de sécurité des agents

Généré depuis les données du dépôt

Combined YAML source

Sources utilisées