CVE-2026-31963
March 18, 2026
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.
Affected Packages
https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) >=1.22 <1.22.2Fix Suggestion:
Update to version 1.22.2https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) =1.23 <1.23.1Fix Suggestion:
Update to version 1.23.1https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) =1.21 <1.21.1Fix Suggestion:
Update to version 1.21.1Related Resources (2)
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Contact UsCVSS v4
Base Score:
8.8
Attack Vector
NETWORK
Attack Complexity
LOW
Attack Requirements
NONE
Privileges Required
NONE
User Interaction
NONE
Vulnerable System Confidentiality
NONE
Vulnerable System Integrity
HIGH
Vulnerable System Availability
LOW
Subsequent System Confidentiality
NONE
Subsequent System Integrity
NONE
Subsequent System Availability
NONE
CVSS v3
Base Score:
8.2
Attack Vector
NETWORK
Attack Complexity
LOW
Privileges Required
NONE
User Interaction
NONE
Scope
UNCHANGED
Confidentiality
NONE
Integrity
HIGH
Availability
LOW
Weakness Type (CWE)
EPSS
Base Score:
0.05