Automic VaultAutomic Vault

brew

bamtools mit Homebrew, apt, MacPorts, Nix installieren

Prüfe Installationswege, Executables, Metadaten und Sicherheitshinweise für bamtools in AI-Agent-Workflows.

InstallationsbefehlSicherheitshinweise

Installation

Weitere Installationsbefehle

macOS

Homebrewverifiziert · 100%
brew install bamtools

local Homebrew formula metadata

MacPortsverifiziert · 94%
sudo port install bamtools

MacPorts ports tree · devel/bamtools/Portfile · Quelle: api.github.com

Linux

Debian aptverifiziert · 92%
sudo apt install bamtools

Debian stable package indexes · bamtools · Quelle: deb.debian.org

Nixverifiziert · 92%
nix profile install nixpkgs#bamtools

nixpkgs package indexes · pkgs/by-name/ba/bamtools/package.nix · Quelle: api.github.com

Überblick

Paketzusammenfassung

C++ API and command-line toolkit for BAM data

Befehle und Aliase

  • bamtools

Verlauf

Projektgeschichte und Nutzung

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.

Projektgeschichte

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.

Adoptionsgeschichte

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.

Wie es verwendet wird

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.

Warum Paket-Nerds sich dafür interessieren

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.

Zeitleiste

  • 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.

Sicherheitslage

Risikostufe: grün

narrow executable package without higher-risk signals.

Risikoklassifikator

grün Risiko · niedrig Konfidenz · appliance

Warum

  • narrow executable package without higher-risk signals

Signale

  • metadata:no-higher-risk-signals

Installationsverhalten

  • In den Formelmetadaten ist kein Homebrew-Post-install-Hook erfasst.
  • Homebrew-Bottle-Metadaten sind für 6 Plattformziele verfügbar.
  • Installiert mit 1 Laufzeitabhängigkeiten.
  • Build-Metadaten listen 2 Build-Abhängigkeiten.

Empfohlene Prüfung

Prüfe vor unbeaufsichtigter Agent-Nutzung, ob das Tool Klartext-Credentials liest, Remote-Zustand schreibt, Artefakte veröffentlicht oder Plugins ausführt.

Executables

Installierte Executables

BefehlArtSichtbarkeitHinweis
bamtoolscliglobales Executable

Aktualität

Version und Aktualität

Diese Signale trennen das Alter der Seitengenerierung, Aktivität des Paketmanagers und Upstream-Release-Vergleich. Versionsrückstand wird nur gemeldet, wenn eine Evidenz-URL und vergleichbare Versionen vorhanden sind.

Seite generiert2026-07-10
Manager-Version2.5.3
Manager aktualisiert2026-05-03
lokale DatenOK
Upstreamaktuell
neueste erkannte Versionv2.5.3

https://github.com/pezmaster31/bamtools

  • OKEs wurden keine Aktualitätswarnungen generiert.

Installationsmetadaten

Paketmetadaten

Paketschlüsselbrew:bamtools
Version2.5.3
PaketmanagerHomebrew
Paketmanager-Seitehttps://formulae.brew.sh/formula/bamtools
Homepagehttps://github.com/pezmaster31/bamtools
Repositoryhttps://github.com/pezmaster31/bamtools
Upstream-Dokumentationhttps://github.com/pezmaster31/bamtools/wiki
LizenzMIT
Quellarchivhttps://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.3.tar.gz
Zuletzt aktualisiert2026-05-03T16:10:34Z
Pulseupdated
Abhängigkeitenjsoncpp
Build-Abhängigkeitencmake, pkgconf
Bottleverfügbar (auf arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
Homebrew post-installnicht definiert
Dienstkeiner deklariert

Registry-Fakten

Details aus der Quelldatenbank

Source DatabaseHomebrew formula API
Taphomebrew/core
Full Namebamtools
Version Scheme0
Revision1
Head VersionHEAD
Bottle Stable Root URLhttps://ghcr.io/v2/homebrew/core
Deprecatedno
Disabledno
Keg Onlyno
URL Keys
  • head
  • stable

Source-Datenbank-Treffer

Andere Paketmanager-Einträge

Treffer stammen aus externen Paketmanager-Indizes und bleiben von lokalen Automic-Vault-Paketlinks getrennt.

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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: bamtools from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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 Abhängigkeiten
  • 1 optionale Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libbamtools2.5.2 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

bamtools

nix profile install nixpkgs#bamtools
  • normalized package name match
  • Abgeglichen nach: Bamtools
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ba/bamtools/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: bamtools from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
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 Abhängigkeiten
  • 1 optionale Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
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 Abhängigkeiten
  • normalized package name match
  • Abgeglichen nach: Bamtools
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libbamtools2.5.2 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
MacPorts95%

bamtools

sudo port install bamtools
  • normalized package name match
  • Abgeglichen nach: Bamtools
MacPorts ports tree · api.github.com · MacPorts ports tree: devel/bamtools/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1

Paketgraph

Links stammen aus dem lokalen Paketbeziehungsgraph, Ergänzungen, Abhängigkeitskanten, Ecosystem-Matches und Paket-Hub-Mitgliedschaft.

Verwandte Tools

  • cmakeBuild dependency declared by Homebrew.
  • pkgconfBuild dependency declared by Homebrew.
  • augustusPopular package that depends on this formula.

Gleicher Workflow

  • perbaseShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • sambambaShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • samtoolsShares av.db curated category or tags: bam, bioinformatics, cli, science.
  • abpoaShares av.db curated category or tags: bioinformatics, cli, science.
  • abricateShares av.db curated category or tags: bioinformatics, cli, science.
  • abyssShares av.db curated category or tags: bioinformatics, cli, science.

Quellspur

Aus Repository-Daten generiert

Diese Seite wird von av-web aus dem privaten Paket-SQLite-Artefakt bereitgestellt, das scripts/generate-pkg-sqlite.py erstellt.

Verwendete Quellen

  • 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