CVE-2026-31963

CVE-2026-31963 is a high-severity vulnerability in Htslib with a CVSS 3.x base score of 8.1. It is not currently listed as actively exploited by CISA, and its EPSS exploit-prediction score is low. The underlying weakness is classified as CWE-122.

Key facts

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.

Frequently asked questions

What is 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.
How severe is CVE-2026-31963?
CVE-2026-31963 has a CVSS 3.x base score of 8.1, rated high severity. It is exploitable over network with low attack complexity, requires no privileges and user interaction. Impact on confidentiality is none, integrity high, and availability high.
Is CVE-2026-31963 being actively exploited?
It is not currently listed in CISA's KEV catalog. Its EPSS exploit-prediction score is 0% (27th percentile), an estimate of the probability of exploitation in the next 30 days.
What products are affected by CVE-2026-31963?
CVE-2026-31963 primarily affects Htslib. In total, 2 product configurations (CPEs) are listed as vulnerable; see the affected-products list for the exact versions.
How do I fix CVE-2026-31963?
Review the linked vendor and NVD advisories for patched versions and mitigations, then upgrade or apply the recommended workaround. Given its high severity, prioritise patching exposed systems.
Does CVE-2026-31963 have an EU (EUVD) identifier?
Yes. CVE-2026-31963 is tracked in the ENISA EU Vulnerability Database (EUVD) as EUVD-2026-12930.
When was CVE-2026-31963 published?
CVE-2026-31963 was published on 2026-03-18 and last updated on 2026-06-17.

References

Affected products (2)

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