# 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 ```sh sudo av install brew:htslib ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install htslib ``` 証拠: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install htslib ``` 証拠: MacPorts ports tree: science/htslib/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - dnf (92%): ```sh sudo dnf install htslib ``` 証拠: Fedora Rawhide package metadata: htslib from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#htslib ``` 証拠: nixpkgs package indexes: pkgs/by-name/ht/htslib/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Debian apt (92%): ```sh sudo apt install htslib-test ``` 証拠: Debian stable package indexes: htslib-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - zypper (92%): ```sh sudo zypper install bgzip ``` 証拠: openSUSE Tumbleweed package metadata: bgzip from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst ## パッケージ情報 - **パッケージキー:** brew:htslib - **パッケージマネージャ:** Homebrew - **バージョン:** 1.24 - **ソース概要:** C library for high-throughput sequencing data formats - **ホームページ:** - **リポジトリ:** - **最終更新:** 2026-07-09T19:51:46Z - **生成日時:** 2026-08-03T19:37:03+00:00 ## 実行可能ファイル - annot-tsv (エイリアス) - bgzip (エイリアス) - htsfile (エイリアス) - ref-cache (エイリアス) - tabix (エイリアス) ## インストール挙動 - Bottle: 利用不可 ## バージョンと鮮度 - ページ生成日: 2026-08-03 - マネージャ版: 1.24 ## 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. ## セキュリティノート library-like package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - library-like package without higher-risk signals ## 他のパッケージマネージャ記録 - Debian apt - htslib-test - 1.21+ds-1: normalized package name match | Debian stable package indexes: htslib-test from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Test data for HTSlib | https://github.com/samtools/htslib - Debian apt - libhts-dev - 1.21+ds-1: normalized package name match | Debian stable package indexes: libhts-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | development files for the HTSlib | https://github.com/samtools/htslib - Debian apt - libhts3t64 - 1.21+ds-1: normalized package name match | Debian stable package indexes: libhts3t64 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | C library for high-throughput sequencing data formats | https://github.com/samtools/htslib - Debian apt - tabix - 1.21+ds-1: normalized package name match | Debian stable package indexes: tabix from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | generic indexer for TAB-delimited genome position files | https://github.com/samtools/htslib - Nix - htslib: normalized package name match | nixpkgs package indexes: pkgs/by-name/ht/htslib/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - htslib-test - 1.19+ds-1.1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: htslib-test from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Test data for HTSlib | https://github.com/samtools/htslib - Ubuntu apt - libhts-dev - 1.19+ds-1.1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: libhts-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | development files for the HTSlib | https://github.com/samtools/htslib - Ubuntu apt - libhts3t64 - 1.19+ds-1.1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: libhts3t64 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | C library for high-throughput sequencing data formats | https://github.com/samtools/htslib - Ubuntu apt - tabix - 1.19+ds-1.1build3: normalized package name match | Ubuntu 24.04 LTS package indexes: tabix from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | generic indexer for TAB-delimited genome position files | https://github.com/samtools/htslib - dnf - htslib - 1.24-1.fc45: normalized package name match | Fedora Rawhide package metadata: htslib from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst | C library for high-throughput sequencing data formats | http://www.htslib.org - dnf - htslib-devel - 1.24-1.fc45: normalized package name match | Fedora Rawhide package metadata: htslib-devel from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst | Development files for htslib | http://www.htslib.org - dnf - htslib-tools - 1.24-1.fc45: normalized package name match | Fedora Rawhide package metadata: htslib-tools from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/07190dc5ae9f35ae73866675fed6d95fe6e8d9fe22c9d7cdf85862cb2ed24a4c-primary.xml.zst | Additional htslib-based tools | http://www.htslib.org - MacPorts - htslib: normalized package name match | MacPorts ports tree: science/htslib/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 - zypper - bgzip - 1.21-1.5: installed executable or alias match | openSUSE Tumbleweed package metadata: bgzip from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst | Block compression/decompression utility from the HTSlib project | https://github.com/samtools/htslib/ - zypper - htsfile - 1.21-1.5: installed executable or alias match | openSUSE Tumbleweed package metadata: htsfile from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst | Identify high-throughput sequencing data files from the HTSlib project | https://github.com/samtools/htslib/ - zypper - tabix - 1.21-1.5: installed executable or alias match | openSUSE Tumbleweed package metadata: tabix from https://download.opensuse.org/tumbleweed/repo/oss/repodata/50b07339cb64c8ed4091bdbabddadc1ff5737b090e478818a195b40d8a3292861a879139b4a3987c31109699fde9fbf4a716367ddf4eef77da75f96e3193d6ed-primary.xml.zst | Generic indexer for TAB-delimited genome position files from the HTSlib project | https://github.com/samtools/htslib/ ## Combined YAML source View the package source record on GitHub. [combined/htslib.yml](https://github.com/mxcl/pkgdb/blob/main/combined/htslib.yml) ## ソース - pkg.so package database - Geiger risk classifier - curated package history - pkgdb category and tag curation - external package-manager database matches - cross-ecosystem install command graph