CVE-2026-31967: HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the ...

Description

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. 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

9.1/10

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

CVSS 4.0

6.9/10

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

0.45%

35.5th 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/9cefb46453ad471e933b8212d4f45920524d3357Patch
https://github.com/samtools/htslib/security/advisories/GHSA-33x5-c6vj-8f2wPatch, Vendor Advisory

Timeline

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

Frequently Asked Questions

What is CVE-2026-31967?

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the `cram_decode_slice()` function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. 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-2026-31967?

CVE-2026-31967 has a CVSS score of 6.9/10 (MEDIUM severity). The EPSS model estimates a 0.45% probability of exploitation in the next 30 days.

How do I fix CVE-2026-31967?

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.