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CVE-2026-31968
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. For the "VARINT" and "CONST" encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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 <1.22.2
Fix Suggestion:
Update to version 1.22.2
https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) =1.23 <1.23.1
Fix Suggestion:
Update to version 1.23.1
https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) =1.21 <1.21.1
Fix Suggestion:
Update to version 1.21.1
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CVSS 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)
Heap-based Buffer Overflow
Out-of-bounds Write
Stack-based Buffer Overflow
Access of Resource Using Incompatible Type ('Type Confusion')
EPSS
Base Score:
0.01