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

Summaryinfo

A vulnerability classified as problematic has been found in samtools htslib up to 1.21.0/1.22.1/1.23. Impacted is the function cram_decode_seq. Performing a manipulation results in out-of-bounds. This vulnerability is cataloged as CVE-2026-31966. It is possible to initiate the attack remotely. There is no exploit available. It is recommended to upgrade the affected component.

Detailsinfo

A vulnerability was found in samtools htslib up to 1.21.0/1.22.1/1.23. It has been classified as critical. This affects the function cram_decode_seq. The manipulation with an unknown input leads to a out-of-bounds vulnerability. CWE is classifying the issue as CWE-125. The product reads data past the end, or before the beginning, of the intended buffer. This is going to have an impact on 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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. 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 shared at github.com. This vulnerability is uniquely identified as CVE-2026-31966 since 03/10/2026. The exploitability is told to be easy. It is possible to initiate the attack remotely. No form of authentication is needed for exploitation. Technical details are known, but no exploit is available.

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-2026-12936). 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

Website

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

CPE 2.3info

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CPE 2.2info

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Exploitinginfo

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Entryinfo

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

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