macOS
Homebrew已验证 · 100%
brew install bamtoolslocal Homebrew formula metadata
MacPorts已验证 · 94%
sudo port install bamtoolsMacPorts ports tree · devel/bamtools/Portfile · 来源: api.github.com
安装
其他安装命令
Linux
Debian apt已验证 · 92%
sudo apt install bamtoolsDebian stable package indexes · bamtools · 来源: deb.debian.org
Nix已验证 · 92%
nix profile install nixpkgs#bamtoolsnixpkgs package indexes · pkgs/by-name/ba/bamtools/package.nix · 来源: api.github.com
概览
软件包摘要
C++ API and command-line toolkit for BAM data
历史
项目历史与用法
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.
项目历史
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.
采用历史
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.
使用方式
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.
为什么软件包爱好者会关心
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.
时间线
- 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.
来源
安全态势
风险级别：绿色
narrow executable package without higher-risk signals.
风险分类器
绿色 风险 · 低 置信度 · appliance
原因
- narrow executable package without higher-risk signals
信号
- metadata:no-higher-risk-signals
安装行为
- formula 元数据中未记录 Homebrew post-install 钩子。
- Homebrew bottle 元数据适用于 6 个平台目标。
- 安装时包含 1 个运行时依赖。
- 构建元数据列出 2 个构建依赖。
建议审查
在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。
可执行文件
已安装的可执行文件
| 命令 | 类型 | 暴露范围 | 备注 |
|---|---|---|---|
bamtools | cli | 全局可执行文件 |
新鲜度
版本和新鲜度
这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。
页面生成时间2026-07-10
管理器版本2.5.3
管理器更新时间2026-05-03
本地数据OK
上游当前
检测到的最新版本v2.5.3
https://github.com/pezmaster31/bamtools
- OK没有生成新鲜度警告。
安装元数据
软件包元数据
| 软件包键 | brew:bamtools |
|---|---|
| 版本 | 2.5.3 |
| 软件包管理器 | Homebrew |
| 软件包管理器页面 | https://formulae.brew.sh/formula/bamtools |
| 主页 | https://github.com/pezmaster31/bamtools |
| 仓库 | https://github.com/pezmaster31/bamtools |
| 上游文档 | https://github.com/pezmaster31/bamtools/wiki |
| 许可证 | MIT |
| 源码归档 | https://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.3.tar.gz |
| 最后更新 | 2026-05-03T16:10:34Z |
| Pulse | updated |
| 依赖 | jsoncpp |
| 构建依赖 | cmake, pkgconf |
| Bottle | 可用 (于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | 未定义 |
| 服务 | 未声明 |
注册表事实
源数据库详情
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | bamtools |
| Version Scheme | 0 |
| Revision | 1 |
| Head Version | HEAD |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
源数据库匹配
其他软件包管理器记录
匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。
Debian apt95%
bamtools 2.5.2+dfsg-6+b1
toolkit for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install bamtools- Section: science
- Architecture: amd64
- Source Package: bamtools
- 5 依赖
- normalized package name match
- 匹配方式：Bamtools
Debian apt95%
libbamtools-dev 2.5.2+dfsg-6+b1
C++ API for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools-dev- Section: libdevel
- Architecture: amd64
- Source Package: bamtools
- 2 依赖
- 1 可选依赖
- normalized package name match
- 匹配方式：Bamtools
Debian apt95%
libbamtools-doc 2.5.2+dfsg-6
docs for dynamic library for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools-doc- Section: doc
- Architecture: all
- Source Package: bamtools
- 1 依赖
- normalized package name match
- 匹配方式：Bamtools
Debian apt95%
libbamtools2.5.2 2.5.2+dfsg-6+b1
dynamic library for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools2.5.2- Section: libs
- Architecture: amd64
- Source Package: bamtools
- 4 依赖
- normalized package name match
- 匹配方式：Bamtools
Nix95%
bamtools
nix profile install nixpkgs#bamtools- normalized package name match
- 匹配方式：Bamtools
Ubuntu apt95%
bamtools 2.5.2+dfsg-4
toolkit for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install bamtools- Section: universe/science
- Architecture: amd64
- 5 依赖
- normalized package name match
- 匹配方式：Bamtools
Ubuntu apt95%
libbamtools-dev 2.5.2+dfsg-4
C++ API for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools-dev- Section: universe/libdevel
- Architecture: amd64
- Source Package: bamtools
- 2 依赖
- 1 可选依赖
- normalized package name match
- 匹配方式：Bamtools
Ubuntu apt95%
libbamtools-doc 2.5.2+dfsg-4
docs for dynamic library for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools-doc- Section: universe/doc
- Architecture: all
- Source Package: bamtools
- 1 依赖
- normalized package name match
- 匹配方式：Bamtools
Ubuntu apt95%
libbamtools2.5.2 2.5.2+dfsg-4
dynamic library for manipulating BAM (genome alignment) files
https://github.com/pezmaster31/bamtools/wiki
sudo apt install libbamtools2.5.2- Section: universe/libs
- Architecture: amd64
- Source Package: bamtools
- 4 依赖
- normalized package name match
- 匹配方式：Bamtools
MacPorts95%
bamtools
sudo port install bamtools- normalized package name match
- 匹配方式：Bamtools
来源线索
由仓库数据生成
此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。
Combined YAML source
View the package source record on GitHub.
使用的来源
- 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