htslib: Stack-based Buffer Overflow
CVE-2026-31968 is a high-severity stack-based buffer overflow vulnerability in htslib from Samtools, with a CVSS 3.1 base score of 8.1 out of 10. It can be exploited remotely over the network by an unauthenticated attacker, but only if a user takes part, for example by opening a link or file. 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 0.47% chance of exploitation within 30 days, which is low compared with other CVEs.
High severity with no evidence of exploitation so far.
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.
- Because the attack needs a user to take part, warn users about unexpected links and files related to this product until it is patched.
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
- RequiredA user must take an action such as opening a file or link.
- Scope
- UnchangedImpact stays within the vulnerable component.
- Confidentiality
- NoneNo data is disclosed.
- Integrity
- HighData or code can be modified at will.
- Availability
- HighThe component can be taken down completely.
Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H. Scored by NVD.
| Scoring system | Score | Severity | Scored by |
|---|---|---|---|
| CVSS 4.0 | 8.8 | High | CNA (github.com) |
| CVSS 3.1 | 8.1 | High | 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 using a variety of encodings and compression methods. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
Source: the CVE record as published by its numbering authority, via NVD and CVE.org.
The underlying weakness: Stack-based Buffer Overflow
The product writes past the end of a buffer that was allocated on the stack.
How developers prevent this class of flaw
- Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index checking. D3-SFCV (Stack Frame Canary Validation) from D3FEND discusses canary-based detection in detail.
- Use an abstraction library to abstract away risky APIs. Not a complete solution.
- Implement and perform bounds checking on input.
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
- 9.1 Critical severity
- 9.1 Critical severity
- 8.2 High severity
Recent Stack-based Buffer Overflow vulnerabilities
- 7.2 High severity
- 7.2 High severity
- 7.8 High severity
- 8.0 High severity
- 7.8 High severity
- 7.8 High severity
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