CVE-2026-31966: Htslib out-of-bounds read (CVSS 9.1)

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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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.

CVSS 3.1 breakdown

Attack vectorNetwork

Attack complexityLow

Privileges requiredNone

User interactionNone

ScopeUnchanged

ConfidentialityHigh

IntegrityNone

AvailabilityHigh

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

Affected products

Htslib≥ 1.22 < 1.22.2 · < 1.21.1 · 1.23

Remediation

Fixed in

Htslib≥ 1.22.2

Patch & vendor advisories

References

Related CVEs

Recent high-severity vulnerabilities sharing a weakness type.

Frequently asked

Is CVE-2026-31966 being actively exploited?

CVE-2026-31966 is not in the CISA KEV catalog. Its EPSS exploit probability is 0.65%.

How severe is CVE-2026-31966?

CVE-2026-31966 has a CVSS 3.1 base score of 9.1, rated critical. EPSS estimates a 0.65% probability of exploitation.

Which products are affected by CVE-2026-31966?

Affected products include Htslib.

How do I fix CVE-2026-31966?

Upgrade affected software to a fixed version, for example Htslib 1.22.2 or later, then confirm no affected versions remain in your inventory.

How Secuno handles this

Secuno correlates vulnerabilities like CVE-2026-31966 against the real software inventory on every managed device, every day. Rather than a static severity, each match is scored in context: exploit availability, EPSS, the asset's exposure, and business criticality decide where it lands in the queue. If an affected version is present anywhere across your portfolio, it surfaces automatically with a prioritised remediation path.

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