High severity · published Mar 18, 2026
CVE-2026-31964
HTSlib CRAM decoder has a NULL Pointer Dereference
7.5
CVSS
0.3%
EPSS
No
On KEV
Description
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.
CVSS vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
None
Confidentiality
None
Integrity
None
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.3% · higher than 27% of CVEs
Exploited in the wildNo evidence yet
CISA KEVNot listed
Ransomware campaign useNot known
Affected products
Which versions
HT
htslib · samtools
< 1.21.1; >= 1.22, < 1.22.2; = 1.23 · source: vendor, NVD
Affected product
HT
htslib
samtools
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