Vulnerability Description
HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. 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.
CVSS Score
HIGH
Affected Products
| Vendor | Product | Versions |
|---|---|---|
| Htslib | Htslib | < 1.21.1 |
Related Weaknesses (CWE)
References
- https://github.com/samtools/htslib/commit/e64e68da567d2309509d059ace016d5d7fc751Patch
- https://github.com/samtools/htslib/security/advisories/GHSA-5w97-85gf-86rmPatchVendor Advisory
FAQ
What is CVE-2026-31964?
CVE-2026-31964 is a vulnerability with a CVSS score of 7.5 (HIGH). HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data using a variety of encodings and compression methods. Whi...
How severe is CVE-2026-31964?
CVE-2026-31964 has been rated HIGH with a CVSS base score of 7.5/10. Review the CVSS metrics above for detailed severity breakdown.
Is there a patch for CVE-2026-31964?
Check the references section above for vendor advisories and patch information. Affected products include: Htslib Htslib.