CVE-2026-31967
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. In the "cram_decode_slice()" function called while reading CRAM records, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. 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) =1.21 <1.21.1Fix Suggestion:
Update to version 1.21.1https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) =1.23 <1.23.1Fix Suggestion:
Update to version 1.23.1Related ResourcesĀ (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
LOW
Vulnerable System Integrity
NONE
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
LOW
Integrity
NONE
Availability
LOW
EPSS
Base Score:
0.02