What’s Vulnerable › Vulnerabilities

CVE-2026-31973: NULL pointer dereference in samtools cram-size

• Severity: high (CVSS 7.5 v3.1)
• Exploited in the wild: not listed in CISA KEV
• EPSS: 0.5% 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-476

Description

SAMtools is a program for reading, manipulating and writing bioinformatics file formats. Starting in version 1.17, in the cram-size command, used to write information about how well CRAM files are compressed, a check to see if the `cram_decode_compression_header()` was missing. If the function returned an error, this could lead to a NULL pointer dereference. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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: from 1.17 through 1.21.1; from 1.22 before 1.22.2; 1.23 — fixed in 1.22.2

How to fix

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

References

• https://github.com/samtools/samtools/commit/06fc2a219b3d7c94d3f412c09f6d1efd51199f2f
• https://github.com/samtools/samtools/security/advisories/GHSA-x86f-q6fj-cm43
• http://www.openwall.com/lists/oss-security/2026/03/18/12

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