Buffer overflow in Htslib
CVE-2026-31963
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.
Vulnerability class: Buffer Overflow
Published · last modified .
CVSS v3 metric
CVSS v3 base score 8.1 (High). Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H.
EPSS exploit prediction
EPSS: 0.005 (41.8th percentile), scored .
Very low probability of exploitation in the next 30 days; routine patching cadence is appropriate. 42nd percentile — 41.8% of CVEs in the catalogue have a lower EPSS than this one. How to read EPSS.
EPSS over last 30 days · oldest: 0.003 · newest: 0.005 · change: +0.002
Affected products
- Htslib — versions 1.23
- Samtools Htslib — versions < 1.21.1, >= 1.22, < 1.22.2, = 1.23
Weakness classification (CWE)
References
Frequently asked questions
- What is CVE-2026-31963?
- CVE-2026-31963 is a high-severity vulnerability in Htslib, classified under Heap-based Buffer Overflow. CVSS score: 8.1/10. Published 2026-03-18.
- How severe is CVE-2026-31963?
- High severity. CVSS v3 base score is 8.1 out of 10.