# bamtools を Homebrew, apt, MacPorts, Nix でインストール bamtools 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:bamtools ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install bamtools ``` 証拠: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install bamtools ``` 証拠: MacPorts ports tree: devel/bamtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install bamtools ``` 証拠: Debian stable package indexes: bamtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - Nix (92%): ```sh nix profile install nixpkgs#bamtools ``` 証拠: nixpkgs package indexes: pkgs/by-name/ba/bamtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## パッケージ情報 - **パッケージキー:** brew:bamtools - **パッケージマネージャ:** Homebrew - **バージョン:** 2.5.3 - **ソース概要:** C++ API and command-line toolkit for BAM data - **ホームページ:** - **リポジトリ:** - **生成日時:** 2026-08-03T19:37:03+00:00 ## 実行可能ファイル - bamtools (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: 2.5.3 ## プロジェクトの歴史と使われ方 BamTools is a C++ API and command-line toolkit for working with BAM files, the binary alignment format used throughout high-throughput sequencing workflows. It is a packaging-significant bioinformatics utility because it provides both reusable libraries and small CLI tools for common BAM inspection and transformation jobs. ### プロジェクトの歴史 The official repository history begins in April 2009 with an initial import by the BamTools maintainers. The README identifies BamTools as both a programmer's API and an end-user toolkit for BAM files and credits Derek Barnett, Erik Garrison, Gabor Marth, and Michael Stromberg in the 2009-2010 copyright notice. The README explicitly acknowledges Heng Li's SAMtools as the original C-language BAM API and toolkit, placing BamTools in the second wave of tooling around the SAM/BAM ecosystem: a C++ library and CLI layer for developers and pipeline authors who wanted BAM manipulation without binding directly to SAMtools internals. BamTools reached the 2.x series by 2011 and has continued to receive maintenance releases, including the 2.5.x line used by modern package managers. ### 採用の歴史 BamTools became a routine distribution package for bioinformatics environments: the supplied package facts list Homebrew, Debian/Ubuntu, MacPorts, and Nix packages. That adoption matters because genomics pipelines often rely on system packages for reproducible command-line utilities on shared clusters and CI images. ### 使われ方 The source tree builds a bamtools toolkit binary with subcommands such as convert, count, coverage, filter, header, index, merge, random, resolve, revert, sort, split, and stats. The same repository also exposes a C++ API for applications that need to read or write BAM data programmatically. Typical users are bioinformatics developers, sequencing pipeline maintainers, and researchers doing command-line BAM file processing outside larger workflow systems. ### パッケージ好きにとっての重要性 For package nerds, BamTools sits at the intersection of library packaging and scientific reproducibility. It is small enough to be a normal Unix package but domain-specific enough that ABI, zlib linkage, and command compatibility matter to downstream genomics stacks. Its relationship to SAMtools makes it historically useful: SAMtools became the canonical C toolkit, while BamTools offered a C++-oriented alternative that distributions could ship for software expecting the BamTools API. ### タイムライン - 2009: Initial BamTools import appears in the official Git history. - 2009-2010: README copyright credits the original BamTools authors. - 2011: v2.0.0 is tagged, establishing the 2.x API/toolkit line. - 2017: v2.5.1 is tagged in the long-lived 2.5 series. - 2025: v2.5.3 is tagged as a maintenance release. ### Related projects - BamTools is directly related to SAMtools and the SAM/BAM file-format ecosystem. It is commonly adjacent to HTSlib/SAMtools-style tooling, alignment pipelines, and downstream genomics packages that consume BAM files. ### ソース - - - - - input.source_facts.package-manager ## セキュリティノート narrow executable package without higher-risk signals. - **Geiger リスク:** グリーン / 低 - narrow executable package without higher-risk signals ## 他のパッケージマネージャ記録 - Debian apt - bamtools - 2.5.2+dfsg-6+b1: normalized package name match | Debian stable package indexes: bamtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | toolkit for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Debian apt - libbamtools-dev - 2.5.2+dfsg-6+b1: normalized package name match | Debian stable package indexes: libbamtools-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | C++ API for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Debian apt - libbamtools-doc - 2.5.2+dfsg-6: normalized package name match | Debian stable package indexes: libbamtools-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | docs for dynamic library for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Debian apt - libbamtools2.5.2 - 2.5.2+dfsg-6+b1: normalized package name match | Debian stable package indexes: libbamtools2.5.2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | dynamic library for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Nix - bamtools: normalized package name match | nixpkgs package indexes: pkgs/by-name/ba/bamtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - bamtools - 2.5.2+dfsg-4: normalized package name match | Ubuntu 24.04 LTS package indexes: bamtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | toolkit for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Ubuntu apt - libbamtools-dev - 2.5.2+dfsg-4: normalized package name match | Ubuntu 24.04 LTS package indexes: libbamtools-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | C++ API for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Ubuntu apt - libbamtools-doc - 2.5.2+dfsg-4: normalized package name match | Ubuntu 24.04 LTS package indexes: libbamtools-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | docs for dynamic library for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - Ubuntu apt - libbamtools2.5.2 - 2.5.2+dfsg-4: normalized package name match | Ubuntu 24.04 LTS package indexes: libbamtools2.5.2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | dynamic library for manipulating BAM (genome alignment) files | https://github.com/pezmaster31/bamtools/wiki - MacPorts - bamtools: normalized package name match | MacPorts ports tree: devel/bamtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## Combined YAML source View the package source record on GitHub. [combined/bamtools.yml](https://github.com/mxcl/pkgdb/blob/main/combined/bamtools.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