CVE-2026-31965

NameCVE-2026-31965
DescriptionHTSlib 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.
SourceCVE (at NVD; CERT, ENISA, LWN, oss-sec, fulldisc, Debian ELTS, Red Hat, Ubuntu, Gentoo, SUSE bugzilla/CVE, GitHub advisories/code/issues, web search, more)

Vulnerable and fixed packages

The table below lists information on source packages.

Source PackageReleaseVersionStatus
htslib (PTS)bullseye1.11-4vulnerable
bookworm1.16+ds-3vulnerable
trixie1.21+ds-1vulnerable
forky, sid1.22.1+ds2-1vulnerable

The information below is based on the following data on fixed versions.

PackageTypeReleaseFixed VersionUrgencyOriginDebian Bugs
htslibsource(unstable)(unfixed)

Notes

https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr
Fixed by: https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357 (1.23.1)

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