Critical severity · published Mar 18, 2026
CVE-2026-31967
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
9.1
CVSS
0.5%
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. 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.
CVSS vector
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H
Attack vector
Network
Complexity
Low
Privileges
None
User interaction
None
Confidentiality
High
Integrity
None
Availability
High
Scope
Unchanged
Exploitation
Is it being used?
Exploit prediction (EPSS)0.5% · higher than 40% 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-2026-31967
CVE.org
https://www.cve.org/CVERecord?id=CVE-2026-31967
Patch
https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357
Patch
https://github.com/samtools/htslib/security/advisories/GHSA-33x5-c6vj-8f2w
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