High severity · published Mar 18, 2026
CVE-2026-31963
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
8.1
CVSS
0.4%
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. 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 these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by 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.
CVSS vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
Required
Confidentiality
None
Integrity
High
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.4% · higher than 30% 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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