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Heap buffer overflow in HTSlib BGZF index file reader

High
daviesrob published GHSA-p345-84hx-fq6q Mar 18, 2026

Package

HTSlib

Affected versions

<= 1.21, 1.22, 1.22.1, 1.23

Patched versions

1.21.1, 1.22.2, 1.23.1

Description

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.

Impact

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.

Patches

Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue.

Workarounds

The easiest work-around is to discard any .gzi index files from untrusted sources, and use the bgzip -r option to recreate them.

References

6dd0d7d

Credits

Thanks to Harrison Green for reporting this issue.

Severity

High

CVSS overall score

This score calculates overall vulnerability severity from 0 to 10 and is based on the Common Vulnerability Scoring System (CVSS).
/ 10

CVSS v4 base metrics

Exploitability Metrics
Attack Vector Network
Attack Complexity Low
Attack Requirements None
Privileges Required None
User interaction Passive
Vulnerable System Impact Metrics
Confidentiality None
Integrity High
Availability Low
Subsequent System Impact Metrics
Confidentiality None
Integrity None
Availability None

CVSS v4 base metrics

Exploitability Metrics
Attack Vector: This metric reflects the context by which vulnerability exploitation is possible. This metric value (and consequently the resulting severity) will be larger the more remote (logically, and physically) an attacker can be in order to exploit the vulnerable system. The assumption is that the number of potential attackers for a vulnerability that could be exploited from across a network is larger than the number of potential attackers that could exploit a vulnerability requiring physical access to a device, and therefore warrants a greater severity.
Attack Complexity: This metric captures measurable actions that must be taken by the attacker to actively evade or circumvent existing built-in security-enhancing conditions in order to obtain a working exploit. These are conditions whose primary purpose is to increase security and/or increase exploit engineering complexity. A vulnerability exploitable without a target-specific variable has a lower complexity than a vulnerability that would require non-trivial customization. This metric is meant to capture security mechanisms utilized by the vulnerable system.
Attack Requirements: This metric captures the prerequisite deployment and execution conditions or variables of the vulnerable system that enable the attack. These differ from security-enhancing techniques/technologies (ref Attack Complexity) as the primary purpose of these conditions is not to explicitly mitigate attacks, but rather, emerge naturally as a consequence of the deployment and execution of the vulnerable system.
Privileges Required: This metric describes the level of privileges an attacker must possess prior to successfully exploiting the vulnerability. The method by which the attacker obtains privileged credentials prior to the attack (e.g., free trial accounts), is outside the scope of this metric. Generally, self-service provisioned accounts do not constitute a privilege requirement if the attacker can grant themselves privileges as part of the attack.
User interaction: This metric captures the requirement for a human user, other than the attacker, to participate in the successful compromise of the vulnerable system. This metric determines whether the vulnerability can be exploited solely at the will of the attacker, or whether a separate user (or user-initiated process) must participate in some manner.
Vulnerable System Impact Metrics
Confidentiality: This metric measures the impact to the confidentiality of the information managed by the VULNERABLE SYSTEM due to a successfully exploited vulnerability. Confidentiality refers to limiting information access and disclosure to only authorized users, as well as preventing access by, or disclosure to, unauthorized ones.
Integrity: This metric measures the impact to integrity of a successfully exploited vulnerability. Integrity refers to the trustworthiness and veracity of information. Integrity of the VULNERABLE SYSTEM is impacted when an attacker makes unauthorized modification of system data. Integrity is also impacted when a system user can repudiate critical actions taken in the context of the system (e.g. due to insufficient logging).
Availability: This metric measures the impact to the availability of the VULNERABLE SYSTEM resulting from a successfully exploited vulnerability. While the Confidentiality and Integrity impact metrics apply to the loss of confidentiality or integrity of data (e.g., information, files) used by the system, this metric refers to the loss of availability of the impacted system itself, such as a networked service (e.g., web, database, email). Since availability refers to the accessibility of information resources, attacks that consume network bandwidth, processor cycles, or disk space all impact the availability of a system.
Subsequent System Impact Metrics
Confidentiality: This metric measures the impact to the confidentiality of the information managed by the SUBSEQUENT SYSTEM due to a successfully exploited vulnerability. Confidentiality refers to limiting information access and disclosure to only authorized users, as well as preventing access by, or disclosure to, unauthorized ones.
Integrity: This metric measures the impact to integrity of a successfully exploited vulnerability. Integrity refers to the trustworthiness and veracity of information. Integrity of the SUBSEQUENT SYSTEM is impacted when an attacker makes unauthorized modification of system data. Integrity is also impacted when a system user can repudiate critical actions taken in the context of the system (e.g. due to insufficient logging).
Availability: This metric measures the impact to the availability of the SUBSEQUENT SYSTEM resulting from a successfully exploited vulnerability. While the Confidentiality and Integrity impact metrics apply to the loss of confidentiality or integrity of data (e.g., information, files) used by the system, this metric refers to the loss of availability of the impacted system itself, such as a networked service (e.g., web, database, email). Since availability refers to the accessibility of information resources, attacks that consume network bandwidth, processor cycles, or disk space all impact the availability of a system.
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N

CVE ID

CVE-2026-31970

Weaknesses

Heap-based Buffer Overflow

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(). Learn more on MITRE.

Incorrect Calculation of Buffer Size

The product does not correctly calculate the size to be used when allocating a buffer, which could lead to a buffer overflow. Learn more on MITRE.

Integer Overflow or Wraparound

The product performs a calculation that can produce an integer overflow or wraparound when the logic assumes that the resulting value will always be larger than the original value. This occurs when an integer value is incremented to a value that is too large to store in the associated representation. When this occurs, the value may become a very small or negative number. Learn more on MITRE.

Out-of-bounds Write

The product writes data past the end, or before the beginning, of the intended buffer. Learn more on MITRE.

Improper Validation of Specified Quantity in Input

The product receives input that is expected to specify a quantity (such as size or length), but it does not validate or incorrectly validates that the quantity has the required properties. Learn more on MITRE.