# CVE-2026-31964: HTSlib CRAM decoder has a NULL Pointer Dereference

> A NULL pointer dereference in HTSlib's CRAM decoder allows attackers to cause a denial of service by providing crafted alignment records.

- **Severity:** Medium 6.9 (`CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/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-2026-31964, GHSA-5w97-85gf-86rm, UBUNTU-CVE-2026-31964

## What is CVE-2026-31964?

CVE-2026-31964 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 using a variety of encodings and compression methods.  While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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-476 (NULL Pointer Dereference)

## Which versions are affected by CVE-2026-31964?

It affects 1 product.


Products: Htslib Htslib.

## How do I fix CVE-2026-31964?

Upgrade to a fixed version.

## Is CVE-2026-31964 being exploited?

There is no known exploitation of CVE-2026-31964 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-2026-31964 and fix it if it is affected.

What it is: CVE-2026-31964 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-2026-31964 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-2026-31964/ (Markdown: https://insights.sbomify.com/CVE-2026-31964/index.md)
```

## Sources

- CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31964
- NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31964
- OSV: https://osv.dev/vulnerability/CVE-2026-31964

---
From sbomify Insights: https://insights.sbomify.com/CVE-2026-31964/
Summaries are generated and may contain mistakes; the official description above is the record.