Automic VaultAutomic Vault

brew

htslib を Homebrew, dnf, MacPorts, Nix, apt, zypper でインストール

htslib のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。

インストールコマンドセキュリティノート

インストール

追加のインストールコマンド

macOS

Homebrew確認済み · 100%
brew install htslib

local Homebrew formula metadata

MacPorts確認済み · 94%
sudo port install htslib

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

Linux

Fedora dnf確認済み · 92%
sudo dnf install htslib

Fedora Rawhide package metadata · htslib · ソース: dl.fedoraproject.org

Nix確認済み · 92%
nix profile install nixpkgs#htslib

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

Debian apt確認済み · 92%
sudo apt install htslib-test

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

openSUSE zypper確認済み · 92%
sudo zypper install bgzip

openSUSE Tumbleweed package metadata · bgzip · ソース: download.opensuse.org

概要

パッケージ概要

C library for high-throughput sequencing data formats

コマンドとエイリアス

  • annot-tsv
  • bgzip
  • htsfile
  • ref-cache
  • tabix

履歴

プロジェクトの歴史と使われ方

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.

プロジェクトの歴史

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.

採用の歴史

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.

使われ方

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.

パッケージ好きにとっての重要性

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.

タイムライン

  • 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.

ソース

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

セキュリティ状態

リスクレベル: グリーン

library-like package without higher-risk signals.

リスク分類器

リスク グリーン · 信頼度 低 · appliance

理由

  • library-like package without higher-risk signals

信号

  • metadata:library-like

インストール挙動

  • formula メタデータに Homebrew post-install フックは記録されていません。
  • Homebrew bottle メタデータは 6 個のプラットフォームターゲットで利用できます。
  • 2 件の実行時依存関係とともにインストールされます。

推奨レビュー

エージェントに無人実行させる前に、このツールが平文の認証情報を読むか、リモート状態を書き込むか、成果物を公開するか、プラグインを起動するかを確認してください。

実行可能ファイル

インストールされる実行可能ファイル

コマンド種類公開範囲メモ
annot-tsvcliグローバル実行可能ファイル
bgzipcliグローバル実行可能ファイル
htsfilecliグローバル実行可能ファイル
ref-cachecliグローバル実行可能ファイル
tabixcliグローバル実行可能ファイル

鮮度

バージョンと鮮度

これらの信号は、ページ生成時期、パッケージマネージャの活動、上流リリース比較を分けて示します。バージョン遅れは、証拠 URL と比較可能なバージョンがある場合だけ警告されます。

ページ生成日2026-07-10
マネージャ版1.24
マネージャ更新日2026-07-09
ローカルデータOK
上流not checked
検出された最新未検出

https://github.com/samtools/htslib

インストールメタデータ

パッケージメタデータ

パッケージキーbrew:htslib
バージョン1.24
パッケージマネージャHomebrew
パッケージマネージャページhttps://formulae.brew.sh/formula/htslib
ホームページhttps://www.htslib.org/
リポジトリhttps://github.com/samtools/htslib
上流ドキュメントhttps://github.com/samtools/htslib#readme
ライセンスMIT AND BSD-3-Clause
ソースアーカイブhttps://github.com/samtools/htslib/releases/download/1.24/htslib-1.24.tar.bz2
最終更新2026-07-09T19:51:46Z
Pulseupdated
依存関係libdeflate, xz
macOS 提供ライブラリbzip2, curl
Bottle利用可能 (対象 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-install未定義
サービス宣言なし

レジストリ情報

ソースデータベース詳細

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namehtslib
Version Scheme0
Revision0
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • stable

ソースデータベース一致

他のパッケージマネージャ記録

一致は外部パッケージマネージャインデックスから取得され、ローカルの Automic Vault パッケージリンクとは分けて表示されます。

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 依存関係
  • normalized package name match
  • 一致条件: 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 依存関係
  • normalized package name match
  • 一致条件: 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 依存関係
  • 1 提供
  • normalized package name match
  • 一致条件: 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 依存関係
  • normalized package name match
  • 一致条件: 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
  • 一致条件: 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 依存関係
  • normalized package name match
  • 一致条件: 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 依存関係
  • normalized package name match
  • 一致条件: 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 依存関係
  • 1 提供
  • normalized package name match
  • 一致条件: 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 依存関係
  • normalized package name match
  • 一致条件: 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 依存関係
  • 2 提供
  • normalized package name match
  • 一致条件: 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 依存関係
  • 2 提供
  • normalized package name match
  • 一致条件: 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 依存関係
  • 1 提供
  • normalized package name match
  • 一致条件: 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
  • 一致条件: 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 依存関係
  • 1 提供
  • installed executable or alias match
  • 一致条件: 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 依存関係
  • 1 提供
  • installed executable or alias match
  • 一致条件: 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 依存関係
  • 1 提供
  • installed executable or alias match
  • 一致条件: 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

パッケージグラフ

リンクは、ローカルのパッケージ関係グラフ、補足データ、依存関係、エコシステム一致、パッケージハブ所属から来ています。

関連ツール

  • libdeflateRuntime dependency declared by Homebrew.
  • xzRuntime dependency declared by Homebrew.
  • augustusPopular package that depends on this formula.
  • bcftoolsPopular package that depends on this formula.
  • freebayesPopular package that depends on this formula.
  • jellyfishPopular package that depends on this formula.
  • samtoolsPopular package that depends on this formula.
  • stringtiePopular package that depends on this formula.

同じワークフロー

  • bbtoolsShares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • bowtie2Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • fgbioShares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • picard-toolsShares av.db curated category or tags: bioinformatics, cli, genomics, sam-bam-cram, science.
  • sambambaShares av.db curated category or tags: bioinformatics, cli, genomics, science, sequencing.
  • abpoaShares av.db curated category or tags: bioinformatics, c-library, cli, science.

エージェント安全ガイド

ソース経路

リポジトリデータから生成

このページは scripts/generate-pkg-sqlite.py が生成した非公開のパッケージ SQLite アーティファクトから av-web によって提供されます。

使用ソース

  • 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