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_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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. There is no workaround for this issue.
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Fixes

Solution

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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_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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. There is no workaround for this issue.
Title HTSlib CRAM decoder has a heap buffer overflow
Weaknesses CWE-122
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: 2026-03-18T20:12:53.495Z

Reserved: 2026-03-10T15:40:10.485Z

Link: CVE-2026-31969

cve-icon Vulnrichment

Updated: 2026-03-18T20:12:46.162Z

cve-icon NVD

Status : Received

Published: 2026-03-18T20:16:21.743

Modified: 2026-03-18T20:16:21.743

Link: CVE-2026-31969

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

No data.

Weaknesses