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. 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. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

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History

Wed, 18 Mar 2026 21:15:00 +0000

Type Values Removed Values Added
Metrics ssvc

{'options': {'Automatable': 'no', 'Exploitation': 'none', 'Technical Impact': 'partial'}, 'version': '2.0.3'}


Wed, 18 Mar 2026 20:00:00 +0000

Type Values Removed Values Added
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. 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. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Title HTSlib CRAM decoder vulnerable to buffer overflow
Weaknesses CWE-121
CWE-122
CWE-1284
CWE-787
References
Metrics cvssV4_0

{'score': 7.1, 'vector': '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'}


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cve-icon MITRE

Status: PUBLISHED

Assigner: GitHub_M

Published:

Updated: 2026-03-18T20:15:22.414Z

Reserved: 2026-03-10T15:40:10.486Z

Link: CVE-2026-31971

cve-icon Vulnrichment

Updated: 2026-03-18T20:15:14.940Z

cve-icon NVD

Status : Received

Published: 2026-03-18T20:16:22.243

Modified: 2026-03-18T20:16:22.243

Link: CVE-2026-31971

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

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