# CVE-2026-31967: HTSlib CRAM reader has out-of-bounds read due to improper validation of input

> An out-of-bounds read in HTSlib's CRAM decoder allows attackers to leak program state or cause crashes via malformed input.

- **Severity:** Medium 6.9 (`CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/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:** Not needed
- **Fix available:** Yes
- **Published:** 18 Mar 2026
- **Updated:** 18 Mar 2026
- **Also known as:** DEBIAN-CVE-2026-31967, GHSA-33x5-c6vj-8f2w, UBUNTU-CVE-2026-31967

## What is CVE-2026-31967?

CVE-2026-31967 is a medium-severity vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim.

### Official description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. 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-129 (Improper Validation of Array Index), CWE-125 (Out-of-bounds Read)

## Which versions are affected by CVE-2026-31967?

It affects 1 product.


Products: Htslib Htslib.

## How do I fix CVE-2026-31967?

Upgrade to a fixed version.

## Is CVE-2026-31967 being exploited?

There is no known exploitation of CVE-2026-31967 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-2026-31967 and fix it if it is affected.

What it is: CVE-2026-31967 is a medium-severity vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim.
Exploitation: There is no known exploitation of CVE-2026-31967 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-2026-31967/ (Markdown: https://insights.sbomify.com/CVE-2026-31967/index.md)
```

## Sources

- CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31967
- NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31967
- OSV: https://osv.dev/vulnerability/CVE-2026-31967

---
From sbomify Insights: https://insights.sbomify.com/CVE-2026-31967/
Summaries are generated and may contain mistakes; the official description above is the record.