Automic VaultAutomic Vault

brew

Installer bamtools avec Homebrew, apt, MacPorts, Nix

Consultez les chemins d'installation, exécutables, métadonnées et notes de sécurité de bamtools pour les workflows d'agents IA.

Commande d'installationNotes de sécurité

installation

Commandes d'installation supplémentaires

macOS

Homebrewvérifié · 100%
brew install bamtools

local Homebrew formula metadata

MacPortsvérifié · 94%
sudo port install bamtools

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

Linux

Debian aptvérifié · 92%
sudo apt install bamtools

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

Nixvérifié · 92%
nix profile install nixpkgs#bamtools

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

aperçu

Résumé du paquet

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

Commandes et alias

  • bamtools

historique

Historique du projet et usages

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.

Historique du projet

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.

Historique d'adoption

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.

Modes d'utilisation

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.

Pourquoi les passionnés de paquets s'y intéressent

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.

Chronologie

  • 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.

posture de sécurité

Niveau de risque : vert

narrow executable package without higher-risk signals.

Classificateur de risque

risque vert · confiance faible · appliance

Pourquoi

  • narrow executable package without higher-risk signals

Signaux

  • metadata:no-higher-risk-signals

Comportement d'installation

  • Aucun hook post-install Homebrew n’est enregistré dans les métadonnées de formule.
  • Les métadonnées de bottle Homebrew sont disponibles pour 6 plateformes.
  • S’installe avec 1 dépendances d’exécution.
  • Les métadonnées de compilation listent 2 dépendances de compilation.

Revue recommandée

Avant une utilisation sans surveillance par un agent, vérifiez si l'outil lit des identifiants en clair, écrit un état distant, publie des artefacts ou lance des plugins.

exécutables

Exécutables installés

CommandeTypeExpositionNote
bamtoolscliexécutable global

fraîcheur

Version et fraîcheur

Ces signaux séparent l'âge de génération de la page, l'activité du gestionnaire de paquets et la comparaison avec les versions amont. Un retard de version n'est signalé que lorsqu'une URL de preuve et des versions comparables sont présentes.

page générée2026-07-10
version du gestionnaire2.5.3
gestionnaire mis à jour2026-05-03
données localesOK
amontà jour
dernière version détectéev2.5.3

https://github.com/pezmaster31/bamtools

  • OKAucun avertissement de fraîcheur n'a été généré.

métadonnées d'installation

Métadonnées du paquet

Clé du paquetbrew:bamtools
Version2.5.3
Gestionnaire de paquetsHomebrew
Page du gestionnaire de paquetshttps://formulae.brew.sh/formula/bamtools
Page d'accueilhttps://github.com/pezmaster31/bamtools
Dépôthttps://github.com/pezmaster31/bamtools
Docs amonthttps://github.com/pezmaster31/bamtools/wiki
LicenceMIT
Archive sourcehttps://github.com/pezmaster31/bamtools/archive/refs/tags/v2.5.3.tar.gz
Dernière mise à jour2026-05-03T16:10:34Z
Pulseupdated
Dépendancesjsoncpp
Dépendances de compilationcmake, pkgconf
Bouteilledisponible (sur arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux)
post-install Homebrewnon défini
Serviceaucun déclaré

faits du registre

Détails de la base source

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

correspondances dans les bases sources

Autres enregistrements de gestionnaires de paquets

Les correspondances proviennent d’index externes de gestionnaires de paquets et restent séparées des liens de paquets Automic Vault locaux.

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 Dépendances
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • 1 dépendances optionnelles
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • normalized package name match
  • Correspondance par : 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
  • Correspondance par : 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 Dépendances
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • 1 dépendances optionnelles
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • normalized package name match
  • Correspondance par : 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 Dépendances
  • normalized package name match
  • Correspondance par : 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
  • Correspondance par : 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

graphe de paquets

Les liens viennent du graphe local de relations entre paquets, des suppléments, des dépendances, des correspondances d'écosystèmes et de l'appartenance aux hubs.

Outils liés

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

Même 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.

piste source

Généré depuis les données du dépôt

Cette page est servie par av-web depuis l'artéfact SQLite privé des paquets généré par scripts/generate-pkg-sqlite.py.

Sources utilisées

  • 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