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CVE-2026-31963 Detail

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.


Metrics

NVD enrichment efforts reference publicly available information to associate vector strings. CVSS information contributed by other sources is also displayed.
CVSS 4.0 Severity and Vector Strings:

NIST CVSS score
NIST: NVD
N/A
NVD assessment not yet provided.

Nist CVSS score does not match with CNA score
CNA:  GitHub, Inc.
CVSS-B 8.8 HIGH
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

References to Advisories, Solutions, and Tools

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URL Source(s) Tag(s)
https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd GitHub, Inc.
https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c GitHub, Inc.

Weakness Enumeration

CWE-ID CWE Name Source
CWE-122 Heap-based Buffer Overflow GitHub, Inc.  
CWE-129 Improper Validation of Array Index GitHub, Inc.  
CWE-787 Out-of-bounds Write GitHub, Inc.  

Change History

1 change records found show changes

Quick Info

CVE Dictionary Entry:
CVE-2026-31963
NVD Published Date:
03/18/2026
NVD Last Modified:
03/18/2026
Source:
GitHub, Inc.