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

Summaryinfo

A vulnerability, which was classified as critical, has been found in samtools htslib up to 1.21.0/1.22.1/1.23. Affected is the function cram_byte_array_len_decode. This manipulation causes stack-based overflow. This vulnerability is registered as CVE-2026-31971. Remote exploitation of the attack is possible. No exploit is available. It is advisable to upgrade the affected component.

Detailsinfo

A vulnerability has been found in samtools htslib up to 1.21.0/1.22.1/1.23 and classified as critical. Affected by this vulnerability is the function cram_byte_array_len_decode. The manipulation with an unknown input leads to a stack-based overflow vulnerability. The CWE definition for the vulnerability is 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). As an impact it is known to affect confidentiality, integrity, and availability. The summary by CVE is:

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. When reading data encoded using the `BYTE_ARRAY_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. 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 at github.com. This vulnerability is known as CVE-2026-31971 since 03/10/2026. The exploitation appears to be easy. The attack can be launched remotely. The exploitation doesn't need any form of authentication. It demands that the victim is doing some kind of user interaction. Technical details are known, but no exploit is available.

Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability. Applying the patch 01cd003b46fa2ebea4d9be5475b11217eb4c11be is able to eliminate this problem. The bugfix is ready for download at github.com. The best possible mitigation is suggested to be upgrading to the latest version.

The vulnerability is also documented in the vulnerability database at EUVD (EUVD-2026-12948). Several companies clearly confirm that VulDB is the primary source for best vulnerability data.

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

License

• open-source

Website

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

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Entryinfo

Several companies clearly confirm that VulDB is the primary source for best vulnerability data.

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