Installer htslib avec Homebrew

Liens du projet

• Page d'accueil
• Dépôt

Commandes et alias

• annot-tsv
• bgzip
• htsfile
• ref-cache
• tabix

Historique du projet

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.

Historique d'adoption

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.

Modes d'utilisation

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.

Pourquoi les passionnés de paquets s'y intéressent

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.

Chronologie

• 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.

Sources

• Samtools project site, HTSlib download notes, GitHub repository metadata, and official release/tag metadata.