CVE-2026-31963

What it is

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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.

At a glance

Exploitability

Can be exploited over the network without logging in. High risk of data tampering.

Exploit odds

0.4% chance of exploitation in the next 30 days (EPSS).

Fix

A patch, advisory or fixed version is referenced. Upgrade or apply it.

Timeline

1. 2026-03-18 19:16 UTC PublishedDisclosed publicly on CVE.org and NVD
2. 2026-06-17 10:34 UTC Last updatedMost recent change to the record

Why it ranks here

• Exploited in the wild: no, CISA does not list it.
• Exploit odds: 0.4% in the next 30 days (EPSS).
• Severity: 8.8 HIGH (CVSS).
• Fix: a patch or advisory is linked.

Details

Published

2026-03-18 19:16 UTC

Last modified

2026-06-17 10:34 UTC

Exploit probability

0.4% · EPSS, next 30 days

Weakness

CWE-122

Record status

Analyzed

Affected

• Htslib < 1.21.1
• Htslib < 1.22.2
• Htslib 1.23

Attack profile CVSS 4.0 · 8.8

Attack vector

Network

Complexity

Low

Attack requirements

None

Privileges needed

None

User interaction

None

Confidentiality

None

Integrity

High

Availability

Low

Is it in your code?

Hand this to your coding agent. It searches your project for the affected products and checks versions. Nothing leaves your machine.

Read https://cve-list.com/agent/cve/CVE-2026-31963.md and follow it. Check whether this project is affected by CVE-2026-31963. Read only. Don't change anything and don't upload my code. Tell me yes, no or not sure, with the file as proof.

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