CVE-2026-31972

NameCVE-2026-31972
DescriptionSAMtools is a program for reading, manipulating and writing bioinformatics file formats. The `mpileup` command outputs DNA sequences that have been aligned against a known reference. On each output line it writes the reference position, optionally the reference DNA base at that position (obtained from a separate file) and all of the DNA bases that aligned to that position. As the output is ordered by position, reference data that is no longer needed is discarded once it has been printed out. Under certain conditions the data could be discarded too early, leading to an attempt to read from a pointer to freed memory. 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. This bug is fixed in versions 1.21.1 and 1.22. 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
samtools (PTS)bullseye1.11-1vulnerable
bookworm1.16.1-1vulnerable
trixie1.21-1vulnerable
forky, sid1.22.1-1vulnerable

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

PackageTypeReleaseFixed VersionUrgencyOriginDebian Bugs
samtoolssource(unstable)(unfixed)

Notes

https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p
Fixed by: https://github.com/samtools/samtools/commit/3036eb9af945fcef359427a2d359855553da4adf

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