CVE-2026-31963 HTSlib CRAM reader has heap buffer overflow due to improper validation of input
An attacker can achieve arbitrary code execution or crash the application by tricking a user into opening a malicious CRAM file processed by HTSlib.
- Exploited in the wild
- Not known
- Login needed
- Not needed
- Attackable
- Over the internet
- Victim action needed
- Not needed
- Fix
- Available
What is CVE-2026-31963?
CVE-2026-31963 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. 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.
Which versions are affected by CVE-2026-31963?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31963?
Upgrade to a fixed version.
Upgrade to the fixed version. Memory-safe languages, compiler hardening and fuzzing prevent most new cases. More about Memory corruption.
Is CVE-2026-31963 being exploited?
There is no known exploitation of CVE-2026-31963 in the wild and no public exploit code.
Other vulnerabilities in samtools htslib
Sources
Also known as DEBIAN-CVE-2026-31963, GHSA-qgqh-h2q9-7w3c, UBUNTU-CVE-2026-31963.