CVE-2026-31971
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. When reading data encoded using the "BYTE_ARRAY_LEN" method, the "cram_byte_array_len_decode()" failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. 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) =1.23 <1.23.1Fix Suggestion:
Update to version 1.23.1https://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) =1.21 <1.21.1Fix Suggestion:
Update to version 1.21.1Related Resources (2)
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Contact UsCVSS v4
Base Score:
7.1
Attack Vector
NETWORK
Attack Complexity
LOW
Attack Requirements
NONE
Privileges Required
NONE
User Interaction
PASSIVE
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:
7.1
Attack Vector
NETWORK
Attack Complexity
LOW
Privileges Required
NONE
User Interaction
REQUIRED
Scope
UNCHANGED
Confidentiality
NONE
Integrity
HIGH
Availability
LOW
Weakness Type (CWE)
EPSS
Base Score:
0.13