CVE-2026-31966

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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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.

At a glance

Exploitability

Can be exploited over the network without logging in. Limited direct impact.

Exploit odds

0.5% 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 20:16 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: 0.5% in the next 30 days (EPSS).
• Severity: 6.9 MEDIUM (CVSS).
• Fix: a patch or advisory is linked.

Details

Published

2026-03-18 20:16 UTC

Last modified

2026-06-17 10:34 UTC

Exploit probability

0.5% · EPSS, next 30 days

Weakness

CWE-125 · Out-of-bounds read

Record status

Analyzed

Affected

• Htslib < 1.21.1
• Htslib < 1.22.2
• Htslib 1.23

Attack profile CVSS 4.0 · 6.9

Attack vector

Network

Complexity

Low

Attack requirements

None

Privileges needed

None

User interaction

None

Confidentiality

Low

Integrity

None

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-2026-31966.md and follow it. Check whether this project is affected by CVE-2026-31966. 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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