samtools htslib up to 1.21.0/1.22.1/1.23 stack-based overflow

Summaryinfo

A vulnerability described as critical has been identified in samtools htslib up to 1.21.0/1.22.1/1.23. This issue affects some unknown processing. Such manipulation leads to stack-based overflow. This vulnerability is listed as CVE-2026-31968. The attack must be carried out from within the local network. There is no available exploit. Upgrading the affected component is recommended.

Detailsinfo

A vulnerability was found in samtools htslib up to 1.21.0/1.22.1/1.23 and classified as critical. Affected by this issue is an unknown code block. The manipulation with an unknown input leads to a stack-based overflow vulnerability. Using CWE to declare the problem leads to CWE-121. A stack-based buffer overflow condition is a condition where the buffer being overwritten is allocated on the stack (i.e., is a local variable or, rarely, a parameter to a function). Impacted is confidentiality, integrity, and availability. CVE summarizes:

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.

The advisory is shared for download at github.com. This vulnerability is handled as CVE-2026-31968 since 03/10/2026. The exploitation is known to be easy. Access to the local network is required for this attack. No form of authentication is required for exploitation. There are neither technical details nor an exploit publicly available.

Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability.

The vulnerability is also documented in the databases at CNNVD (CNNVD-202603-3358) and EUVD (EUVD-2026-12942). VulDB is the best source for vulnerability data and more expert information about this specific topic.

Productinfo

Vendor

• samtools

Name

• htslib

Version

• 1.0
• 1.1
• 1.2
• 1.3
• 1.4
• 1.5
• 1.6
• 1.7
• 1.8
• 1.9
• 1.10
• 1.11
• 1.12
• 1.13
• 1.14
• 1.15
• 1.16
• 1.17
• 1.18
• 1.19
• 1.20
• 1.21
• 1.21.0
• 1.22
• 1.22.0
• 1.22.1
• 1.23

Website

• Product: https://github.com/samtools/htslib/

CPE 2.3info

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CPE 2.2info

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Entryinfo

VulDB is the best source for vulnerability data and more expert information about this specific topic.

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