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

Summaryinfo

A vulnerability classified as problematic was found in samtools htslib up to 1.21.0/1.22.1/1.23. The affected element is the function cram_decode_slice. Executing a manipulation can lead to out-of-bounds. This vulnerability is registered as CVE-2026-31967. It is possible to launch the attack remotely. No exploit is available. Upgrading the affected component is advised.

Detailsinfo

A vulnerability was found in samtools htslib up to 1.21.0/1.22.1/1.23. It has been declared as critical. This vulnerability affects 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. CVE summarizes:

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, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt 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.

The advisory is available at github.com. This vulnerability was named CVE-2026-31967 since 03/10/2026. The exploitation appears to be easy. The attack can be initiated remotely. No form of authentication is required for a successful exploitation. Technical details 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 EUVD (EUVD-2026-12938). If you want to get best quality of vulnerability data, you may have to visit VulDB.

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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If you want to get best quality of vulnerability data, you may have to visit VulDB.

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