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

> A heap buffer overflow in HTSlib's CRAM decoder allows attackers to execute arbitrary code or crash the application by tricking users into opening a malicious file.

- **Severity:** High 7.1 (`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`)
- **Exploited in the wild:** Not known
- **Login needed:** Not needed
- **Attackable:** Over the internet
- **Victim action needed:** A user has to click or open something
- **Fix available:** Yes
- **Published:** 18 Mar 2026
- **Updated:** 18 Mar 2026
- **Also known as:** DEBIAN-CVE-2026-31969, GHSA-q4cj-f4h5-fqgc, UBUNTU-CVE-2026-31969

## What is CVE-2026-31969?

CVE-2026-31969 is a high-severity memory corruption vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, and only if a user opens a file or follows a link.

### Official 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.

Weakness: CWE-787 (Out-of-bounds Write), CWE-122 (Heap-based Buffer Overflow)

## Which versions are affected by CVE-2026-31969?

It affects 1 product.


Products: Htslib Htslib.

## How do I fix CVE-2026-31969?

Upgrade to a fixed version.

## Is CVE-2026-31969 being exploited?

There is no known exploitation of CVE-2026-31969 in the wild and no public exploit code.

## Other vulnerabilities in samtools htslib

- [CVE-2018-13845](https://insights.sbomify.com/CVE-2018-13845/): Memory corruption in n/a (critical 9.8)
- [CVE-2017-1000206](https://insights.sbomify.com/CVE-2017-1000206/): Memory corruption in n/a (critical 9.8)
- [CVE-2026-31962](https://insights.sbomify.com/CVE-2026-31962/): HTSlib CRAM reader has heap buffer overflow due to improper validation of input (high 8.8)
- [CVE-2026-31963](https://insights.sbomify.com/CVE-2026-31963/): HTSlib CRAM reader has heap buffer overflow due to improper validation of input (high 8.8)
- [CVE-2026-31968](https://insights.sbomify.com/CVE-2026-31968/): HTSlib CRAM decoder vulnerable to buffer overflow (high 8.8)

## Fix prompt for AI coding agents

```text
Check this codebase for CVE-2026-31969 and fix it if it is affected.

What it is: CVE-2026-31969 is a high-severity memory corruption vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, and only if a user opens a file or follows a link.
Exploitation: There is no known exploitation of CVE-2026-31969 in the wild and no public exploit code.

Affected product: samtools htslib. No package-level version data is available, so check the vendor advisory linked from the reference page.

Task:
1. Search the dependency manifests and lockfiles (for example package.json, package-lock.json, requirements.txt, poetry.lock, uv.lock, pom.xml, build.gradle, go.mod, Cargo.lock, Gemfile.lock) and any Dockerfiles for the affected packages, including transitive dependencies.
2. If an affected version is in use, upgrade it to the fixed version for its release line with the project's package manager, so the lockfile is regenerated. Prefer the smallest upgrade that fixes it.
3. If there is no fix, or the upgrade would break the build, do not guess: explain the risk and the safest workaround instead.
4. Run the tests and summarise what changed and why.
5. If nothing in the project is affected, say so and change nothing.

Reference: https://insights.sbomify.com/CVE-2026-31969/ (Markdown: https://insights.sbomify.com/CVE-2026-31969/index.md)
```

## Sources

- CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31969
- NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31969
- OSV: https://osv.dev/vulnerability/CVE-2026-31969

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From sbomify Insights: https://insights.sbomify.com/CVE-2026-31969/
Summaries are generated and may contain mistakes; the official description above is the record.