SAMtools up to 1.21.0/1.22.1/1.23 CRAM File Parser cram_decode_compression_header null pointer dereference

Summaryinfo

A vulnerability was found in SAMtools up to 1.21.0/1.22.1/1.23. It has been rated as problematic. Impacted is the function cram_decode_compression_header of the component CRAM File Parser. This manipulation causes null pointer dereference. This vulnerability is handled as CVE-2026-31973. The attack can be initiated remotely. There is not any exploit available. Upgrading the affected component is advised.

Detailsinfo

A vulnerability classified as critical was found in SAMtools up to 1.21.0/1.22.1/1.23. Affected by this vulnerability is the function cram_decode_compression_header of the component CRAM File Parser. The manipulation with an unknown input leads to a null pointer dereference vulnerability. The CWE definition for the vulnerability is CWE-476. A NULL pointer dereference occurs when the application dereferences a pointer that it expects to be valid, but is NULL, typically causing a crash or exit. As an impact it is known to affect integrity, and availability. The summary by CVE is:

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.

It is possible to read the advisory at github.com. This vulnerability is known as CVE-2026-31973 since 03/10/2026. The exploitation appears to be easy. The attack can be launched remotely. The exploitation doesn't need any form of authentication. Technical details of the vulnerability are known, but there is no available exploit.

Upgrading to version 1.21.1 or 1.22.2 eliminates this vulnerability. Applying the patch 06fc2a219b3d7c94d3f412c09f6d1efd51199f2f is able to eliminate this problem. The bugfix is ready for download at github.com. The best possible mitigation is suggested to be upgrading to the latest version.

The vulnerability is also documented in the vulnerability database at EUVD (EUVD-2026-12958). Be aware that VulDB is the high quality source for vulnerability data.

Productinfo

Name

• SAMtools

Version

• 1.0
• 1.1
• 1.2
• 1.3
• 1.4
• 1.5
• 1.6
• 1.7
• 1.8
• 1.9
• 1.10
• 1.11
• 1.12
• 1.13
• 1.14
• 1.15
• 1.16
• 1.17
• 1.18
• 1.19
• 1.20
• 1.21
• 1.21.0
• 1.22
• 1.22.0
• 1.22.1
• 1.23

License

• open-source

Website

• Product: https://github.com/samtools/samtools/

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Be aware that VulDB is the high quality source for vulnerability data.

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