samtools htslib up to 1.21.0/1.22.1/1.23 cram_decode_slice out-of-bounds

Summaryinfo

A vulnerability marked as problematic has been reported in samtools htslib up to 1.21.0/1.22.1/1.23. This vulnerability affects the function cram_decode_slice. This manipulation causes out-of-bounds. This vulnerability is tracked as CVE-2026-31965. The attack is possible to be carried out remotely. No exploit exists. It is suggested 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_decode_slice. The manipulation with an unknown input leads to a out-of-bounds vulnerability. The CWE definition for the vulnerability is CWE-125. The product reads data past the end, or before the beginning, of the intended buffer. 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. In the `cram_decode_slice()` function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying 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.

It is possible to read the advisory at github.com. This vulnerability is known as CVE-2026-31965 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. Technical details of the vulnerability are known, but there is no available exploit.

Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability.

The vulnerability is also documented in the vulnerability database at CNNVD (CNNVD-202603-3362). Be aware that VulDB is the high quality source for 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

Website

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

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Be aware that VulDB is the high quality source for vulnerability data.

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