HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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 18:45:00 +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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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-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: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: 2026-03-18T18:52:43.260Z

Reserved: 2026-03-10T15:40:10.484Z

Link: CVE-2026-31963

cve-icon Vulnrichment

Updated: 2026-03-18T18:52:37.229Z

cve-icon NVD

Status : Received

Published: 2026-03-18T19:16:04.440

Modified: 2026-03-18T19:16:04.440

Link: CVE-2026-31963

cve-icon Redhat

No data.

cve-icon OpenCVE Enrichment

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Weaknesses