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Install htslib with Homebrew
C library for high-throughput sequencing data formats. Version 1.24 via Homebrew; verified 2026-07-09.
install
Additional install commands
overview
Package summary
C library for high-throughput sequencing data formats
Project links
Commands and aliases
- annot-tsv
- bgzip
- htsfile
- ref-cache
- tabix
history
Project history and usage
HTSlib is the C library layer of the Samtools family, providing shared reading and writing support for high-throughput sequencing formats such as SAM, BAM, CRAM, VCF, and BCF. It matters beyond a single command-line package because many genomics tools build on the same file-format and indexing behavior.
Project history
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.
Adoption history
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.
How it is used
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.
Why package nerds care
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.
Timeline
- 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.
security posture
Risk level: green
library-like package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- library-like package without higher-risk signals
Signals
- metadata:library-like
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
annot-tsv | executable | indexed executable | Discovered from the local executable index. |
bgzip | executable | indexed executable | Discovered from the local executable index. |
htsfile | executable | indexed executable | Discovered from the local executable index. |
ref-cache | executable | indexed executable | Discovered from the local executable index. |
tabix | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version1.24
manager updated2026-07-09
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:htslib |
|---|---|
| Version | 1.24 |
| Package manager | Homebrew |
| Homepage | https://www.htslib.org/ |
| Repository | https://github.com/samtools/htslib |
| Last updated | 2026-07-09T19:51:46Z |
| Pulse | updated |
| Bottle | not recorded |
| Service | none declared |
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- Nucleus package database
- curated package history
- pkgdb category and tag curation