CVE-2026-31964
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 using a variety of encodings and compression methods. 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 "CONST", "XPACK" and "XRLE" encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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) =1.23 <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 1.21.1https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) >=1.22 <1.22.2Fix Suggestion:
Update to version 1.22.2Related Resources (2)
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Contact UsCVSS v4
Base Score:
6.9
Attack Vector
NETWORK
Attack Complexity
LOW
Attack Requirements
NONE
Privileges Required
NONE
User Interaction
NONE
Vulnerable System Confidentiality
NONE
Vulnerable System Integrity
LOW
Vulnerable System Availability
LOW
Subsequent System Confidentiality
NONE
Subsequent System Integrity
NONE
Subsequent System Availability
NONE
CVSS v3
Base Score:
6.5
Attack Vector
NETWORK
Attack Complexity
LOW
Privileges Required
NONE
User Interaction
NONE
Scope
UNCHANGED
Confidentiality
NONE
Integrity
LOW
Availability
LOW
Weakness Type (CWE)
NULL Pointer Dereference
EPSS
Base Score:
0.04