# CVE-2026-31973: NULL pointer dereference in samtools cram-size

> A missing error check in samtools cram-size allows a NULL pointer dereference, causing the application to crash when processing malformed CRAM files.

- **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:** No
- **Published:** 18 Mar 2026
- **Updated:** 19 Mar 2026
- **Also known as:** DEBIAN-CVE-2026-31973, GHSA-x86f-q6fj-cm43, UBUNTU-CVE-2026-31973

## What is CVE-2026-31973?

CVE-2026-31973 is a medium-severity vulnerability in samtools, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim.

### Official description

SAMtools is a program for reading, manipulating and writing bioinformatics file formats. Starting in version 1.17, in the cram-size command, used to write information about how well CRAM files are compressed, a check to see if the `cram_decode_compression_header()` was missing. If the function returned an error, this could lead to a NULL pointer dereference. 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-2026-31973?

It affects 1 product.


Products: Samtools Samtools.

## How do I fix CVE-2026-31973?

No fix has been published for CVE-2026-31973 yet. Limit exposure of the affected software until one is available.

## Is CVE-2026-31973 being exploited?

There is no known exploitation of CVE-2026-31973 in the wild and no public exploit code.

## Other vulnerabilities in samtools

- [CVE-2026-31972](https://insights.sbomify.com/CVE-2026-31972/): samtools mpileup has use-after-free leading to an invalid read (medium 6.9)

## Fix prompt for AI coding agents

```text
Check this codebase for CVE-2026-31973 and fix it if it is affected.

What it is: CVE-2026-31973 is a medium-severity vulnerability in samtools, 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-2026-31973 in the wild and no public exploit code.

Affected product: samtools. 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-2026-31973/ (Markdown: https://insights.sbomify.com/CVE-2026-31973/index.md)
```

## Sources

- CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31973
- NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31973
- OSV: https://osv.dev/vulnerability/CVE-2026-31973

---
From sbomify Insights: https://insights.sbomify.com/CVE-2026-31973/
Summaries are generated and may contain mistakes; the official description above is the record.