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CVE-2026-31966
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 CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the "cram_decode_seq()" function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM "MD" tag. This allowed arbitrary data to be leaked to the calling function. 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) =1.23 <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
https://github.com/samtools/htslib.git (GITHUB):
Affected version(s) >=1.22 <1.22.2
Fix Suggestion:
Update to version 1.22.2
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CVSS 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
Weakness Type (CWE)
Out-of-bounds Read
Improper Validation of Array Index
EPSS
Base Score:
0.01