CVE-2026-31964: HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a ...

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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

7.5/10

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

CVSS 4.0

6.9/10

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

0.32%

24.0th percentile

Probability of exploitation in the next 30 days. Learn more

Weakness Enumeration

CWE-476

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/e64e68da567d2309509d059ace016d5d7fc7514fPatch
https://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rmPatch, Vendor Advisory

Timeline

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

Frequently Asked Questions

What is CVE-2026-31964?

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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-2026-31964?

CVE-2026-31964 has a CVSS score of 6.9/10 (MEDIUM severity). The EPSS model estimates a 0.32% probability of exploitation in the next 30 days.

How do I fix CVE-2026-31964?

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.