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Buffer overflow vulnerabilities in HTSlib CRAM decoder

High
daviesrob published GHSA-jvx4-4wq7-6fmh 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. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. When reading data encoded using the BYTE_ARRAY_LEN method, the cram_byte_array_len_decode() failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes.

Impact

Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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

There is no workaround for this issue.

References

01cd003

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-2026-31971

Weaknesses

Stack-based Buffer Overflow

A stack-based buffer overflow condition is a condition where the buffer being overwritten is allocated on the stack (i.e., is a local variable or, rarely, a parameter to a function). Learn more on MITRE.

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.

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.