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

Medium 6.9 Published 18 Mar 2026 Updated 18 Mar 2026

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

Exploited in the wild: Not known
Login needed: Not needed
Attackable: Over the internet
Victim action needed: Not needed
Fix: Available

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

Which versions are affected by CVE-2026-31964?

It affects 1 product.

Products include 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.

Sources

Also known as DEBIAN-CVE-2026-31964, GHSA-5w97-85gf-86rm, UBUNTU-CVE-2026-31964.