CVE-2026-31972: samtools <= 1.21 Use-after-free in mpileup leading to an invalid read

[Robert Davies <rmd () sanger ac uk>]

Description
-----------

SAMtools 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.

Impact
------

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.

Severity
--------

Moderate CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N

Patches
-------

This bug is fixed in versions 1.21.1 and 1.22

Workarounds
-----------

There is no workaround for this issue.

References
----------

https://github.com/samtools/samtools/security/advisories/GHSA-72c8-4jf3-f27p
https://www.cve.org/CVERecord?id=CVE-2026-31972

--

The SAMtools team   https://www.htslib.org/  https://www.sanger.ac.uk/


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