CVE-2026-31962: HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While m...

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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

8.8/10

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

CVSS 4.0

8.8/10

CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/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

0.36%

28.0th 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/d799b54c6401879187bba4741be83ff590ac73e3Patch
https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwpPatch, Vendor Advisory

Timeline

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

Frequently Asked Questions

What is CVE-2026-31962?

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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-2026-31962?

CVE-2026-31962 has a CVSS score of 8.8/10 (HIGH severity). The EPSS model estimates a 0.36% probability of exploitation in the next 30 days.

How do I fix CVE-2026-31962?

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.