samtools htslib up to 1.21.0/1.22.1/1.23 GZI File Parser bgzf_index_load_hfile heap-based overflow

Summaryinfo

A vulnerability was found in samtools htslib up to 1.21.0/1.22.1/1.23. It has been classified as critical. Affected by this vulnerability is the function bgzf_index_load_hfile of the component GZI File Parser. Performing a manipulation results in heap-based overflow. This vulnerability is known as CVE-2026-31970. Remote exploitation of the attack is possible. No exploit is available. Upgrading the affected component is recommended.

Detailsinfo

A vulnerability, which was classified as critical, was found in samtools htslib up to 1.21.0/1.22.1/1.23. This affects the function bgzf_index_load_hfile of the component GZI File Parser. The manipulation with an unknown input leads to a heap-based overflow vulnerability. CWE is classifying the issue as CWE-122. A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc(). 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. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by 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. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.

It is possible to read the advisory at github.com. This vulnerability is uniquely identified as CVE-2026-31970 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. It demands that the victim is doing some kind of user interaction. 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. Applying the patch 6dd0d7d0e9e7e2e173a28969e624db8bc8bb5828 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-2026-12946). 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

License

• open-source

Website

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

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Entryinfo

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

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