CVE intelligence and bounded remediation

CVE-2026-31972 — SAMtools is a program for reading, manipulating and writing bioinformatics file formats

Critical CVSS 9.8

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. 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.

Severity
Critical
CVSS
9.8 (3.1)
Published
2026-03-18
CISA KEV
Not currently listed
Ecosystem
software/application
Weaknesses
CWE-416

Affected products

  • samtools / samtools

Matched remediation archetype

Use-after-free, double free, and expired resource use

This catalog composition supplies bounded fallback guidance. Explicitly reviewed curated workflows load with the complete record below.

Check exposure

  • Trace ownership, references, callbacks, asynchronous tasks, and teardown paths around the affected object or resource.
  • Identify reachable inputs and timing or state transitions that can release the object while references remain.
  • Confirm affected builds, allocators, feature flags, architectures, and process privileges.

Remediate safely

  • Apply the maintained ownership or lifetime fix and rebuild all artifacts containing the affected native code.
  • Use explicit ownership, safe reference management, cancellation and join semantics, and idempotent teardown.
  • Add deterministic lifetime tests plus isolated sanitizer and concurrency coverage for shutdown and error paths.

Authoritative sources

Complete CVE record and remediation plan

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