CVE-2026-31965: HTSlib CRAM reader has out-of-bounds reads due to improper validation of input

Severity: high (CVSS 8.2 v3.1)
Exploited in the wild: not listed in CISA KEV
EPSS: 0.4% probability of exploitation in the next 30 days
Public exploit or detection template: none known
Published: 2026-03-18 · updated 2026-06-17
Weakness: CWE-125

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, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying 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 products

samtools htslib: before 1.21.1; from 1.22 before 1.22.2; 1.23 — fixed in 1.21.1, 1.22.2

How to fix

Upgrade to a fixed version: samtools htslib 1.21.1, 1.22.2. Check the vendor advisory for mitigations.

References

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