# CVE-2026-31962: HTSlib CRAM reader has heap buffer overflow due to improper validation of input

> A heap buffer overflow in HTSlib's CRAM reader allows attackers to execute arbitrary code or crash the application by providing a maliciously crafted file.

- **Severity:** High 8.8 (`CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/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:** Not needed
- **Fix available:** Yes
- **Published:** 18 Mar 2026
- **Updated:** 18 Mar 2026
- **Also known as:** DEBIAN-CVE-2026-31962, GHSA-xxmp-v7h3-gpwp, OESA-2026-2547, OESA-2026-2757, OESA-2026-3491, UBUNTU-CVE-2026-31962

## What is CVE-2026-31962?

CVE-2026-31962 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, 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. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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-129 (Improper Validation of Array Index), CWE-125 (Out-of-bounds Read), CWE-122 (Heap-based Buffer Overflow)

## Which versions are affected by CVE-2026-31962?

It affects 1 product.


Products: Htslib Htslib.

## How do I fix CVE-2026-31962?

Upgrade to a fixed version.

## Is CVE-2026-31962 being exploited?

There is no known exploitation of CVE-2026-31962 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-2026-31963](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)
- [CVE-2020-36403](https://insights.sbomify.com/CVE-2020-36403/): Memory corruption in n/a (high 8.8)

## Fix prompt for AI coding agents

```text
Check this codebase for CVE-2026-31962 and fix it if it is affected.

What it is: CVE-2026-31962 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, with no action from the victim.
Exploitation: There is no known exploitation of CVE-2026-31962 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-2026-31962/ (Markdown: https://insights.sbomify.com/CVE-2026-31962/index.md)
```

## Sources

- CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31962
- NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31962
- OSV: https://osv.dev/vulnerability/CVE-2026-31962

---
From sbomify Insights: https://insights.sbomify.com/CVE-2026-31962/
Summaries are generated and may contain mistakes; the official description above is the record.