PT-2026-26141 · Samtools · Htslib

Published 2026-03-18 · Updated 2026-03-18 · CVE-2026-31965

NVD

CVSS v4.0

6.9

Medium

AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. In the cram decode slice() function called while reading CRAM records, validation of the reference id field occurred too late, allowing two out of bounds reads to occur before the invalid data was detected. The bug does allow two values to be leaked to the caller, however as the function reports an error it may be difficult to exploit them. It is also possible that the program will crash due to trying to access invalid memory. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

Fix

Improper Validation of Array Index

Out of bounds Read

Weakness Enumeration

CWE-129

CWE-125

Related Identifiers

CVE-2026-31965

Affected Products

Htslib

References · 3

• https://nvd.nist.gov/vuln/detail/CVE-2026-31965 · Security Note
• https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhr · Note
• https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357 · Note