htslib: Out-of-bounds Read
CVE-2026-31966 is a critical-severity out-of-bounds read vulnerability in htslib from Samtools, with a CVSS 3.1 base score of 9.1 out of 10. It can be exploited remotely over the network by an unauthenticated attacker, without any action from a user. Affected htslib versions: < 1.21.1; >= 1.22, < 1.22.2; = 1.23. The record does not name a fixed version, so check the vendor advisory. There is no confirmed exploitation so far. EPSS estimates a 0.58% chance of exploitation within 30 days, which is low compared with other CVEs.
Critical severity: a successful attack would have severe impact.
What to do
- Check which version of htslib you run against the affected versions below, and install the vendor's latest release.
- Read the advisory on github.com for workarounds and exact fixed builds.
- Until you can update, restrict network access to the affected service so it is not reachable from untrusted networks.
Affected products and versions
Version data comes from the organisation that assigned the CVE. Confirm against the vendor advisory before deciding you are unaffected.
How the severity score breaks down
- Attack vector
- NetworkCan be exploited remotely over a network, including the internet.
- Attack complexity
- LowNo special conditions are needed; the attack works reliably.
- Privileges required
- NoneNo account or login is needed.
- User interaction
- NoneNo action by a victim is required.
- Scope
- UnchangedImpact stays within the vulnerable component.
- Confidentiality
- HighAll data handled by the component can be read.
- Integrity
- NoneNothing can be modified.
- Availability
- HighThe component can be taken down completely.
Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H. Scored by NVD.
| Scoring system | Score | Severity | Scored by |
|---|---|---|---|
| CVSS 4.0 | 6.9 | Medium | CNA (github.com) |
| CVSS 3.1 | 9.1 | Critical | NVD |
Official 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.
Source: the CVE record as published by its numbering authority, via NVD and CVE.org.
The underlying weakness: Out-of-bounds Read
The product reads data past the end, or before the beginning, of the intended buffer.
How developers prevent this class of flaw
- Use a language that provides appropriate memory abstractions.
Timeline
- CVE record published.
- CISA published its SSVC assessment (exploitation: none, automatable: yes, technical impact: partial).
- Record last changed materially (score, affected products, status or references).
References
Patches and release notes
Other vulnerabilities in htslib
- 8.1 High severity
- 8.1 High severity
- 8.1 High severity
- 8.1 High severity
- 9.1 Critical severity
- 8.2 High severity
Recent Out-of-bounds Read vulnerabilities
- 7.1 High severity
- 7.1 High severity
- 7.1 High severity
- 7.1 High severity
- 7.1 High severity
- 7.1 High severity
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