htslib: NULL Pointer Dereference
CVE-2026-31964 is a high-severity NULL pointer dereference vulnerability in htslib from Samtools, with a CVSS 3.1 base score of 7.5 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 0.38% 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.
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
- NoneNo data is disclosed.
- 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:N/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 | 7.5 | 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. 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.
Source: the CVE record as published by its numbering authority, via NVD and CVE.org.
The underlying weakness: NULL Pointer Dereference
The product dereferences a pointer that it expects to be valid but is NULL.
How developers prevent this class of flaw
- For any pointers that could have been modified or provided from a function that can return NULL, check the pointer for NULL before use. When working with a multithreaded or otherwise asynchronous environment, ensure that proper locking APIs are used to lock before the check, and unlock when it has finished.
- Select a programming language that is not susceptible to these issues.
- Check the results of all functions that return a value and verify that the value is non-null before acting upon it.
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
- 9.1 Critical severity
Recent NULL Pointer Dereference vulnerabilities
- 7.5 High severity
- 7.5 High severity
- 7.8 High severity
- 7.5 High severity
- 7.5 High severity
- 7.5 High severity
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