HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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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History

Wed, 18 Mar 2026 19:15:00 +0000

Type Values Removed Values Added
Metrics ssvc

{'options': {'Automatable': 'yes', 'Exploitation': 'none', 'Technical Impact': 'partial'}, 'version': '2.0.3'}


Wed, 18 Mar 2026 18:15:00 +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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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 reader has heap buffer overflow due to improper validation of input
Weaknesses CWE-122
CWE-125
CWE-129
CWE-787
References
Metrics cvssV4_0

{'score': 8.8, 'vector': 'CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:H/VA:L/SC:N/SI:N/SA:N'}


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cve-icon MITRE

Status: PUBLISHED

Assigner: GitHub_M

Published:

Updated: 2026-03-18T18:37:22.954Z

Reserved: 2026-03-10T15:40:10.483Z

Link: CVE-2026-31962

cve-icon Vulnrichment

Updated: 2026-03-18T18:37:19.990Z

cve-icon NVD

Status : Received

Published: 2026-03-18T18:16:28.190

Modified: 2026-03-18T18:16:28.190

Link: CVE-2026-31962

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

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