High severity · published Mar 18, 2026
CVE-2026-31962
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
8.8
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. 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 `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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:H/I:H/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
Required
Confidentiality
High
Integrity
High
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.4% · higher than 31% 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
References
NVD
https://nvd.nist.gov/vuln/detail/CVE-2026-31962
CVE.org
https://www.cve.org/CVERecord?id=CVE-2026-31962
Patch
https://github.com/samtools/htslib/commit/d799b54c6401879187bba4741be83ff590ac73e3
Patch
https://github.com/samtools/htslib/security/advisories/GHSA-xxmp-v7h3-gpwp
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