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 ...

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.

Metrics

CVSS 3.1

8.1/10

CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H

CVSS 4.0

8.8/10

CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X

EPSS Probability

0.35%

26.7th percentile

Probability of exploitation in the next 30 days. Learn more

Weakness Enumeration

Affected Software

Vendor	Product	Versions
Htslib	Htslib	< 1.21.1
Htslib	Htslib	>= 1.22, < 1.22.2
Htslib	Htslib	1.23

References

https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acdPatch
https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3cPatch, Vendor Advisory

Timeline

Published: Mar 18, 2026
Last Modified: Jun 17, 2026
Status: Analyzed

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 score of 8.8/10 (HIGH severity). The EPSS model estimates a 0.35% probability of exploitation in the next 30 days.

How do I fix CVE-2026-31963?

Check the vendor references and advisories linked above for patched versions and mitigation guidance. You can also run a Strix scan to test if your systems are affected.