CVE-2026-31965

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.

• CWE-125
• CWE-129

• https://github.com/samtools/htslib/commit/9cefb46453ad471e933b8212d4f45920524d3357Patch
• https://github.com/samtools/htslib/security/advisories/GHSA-mqm2-v645-3qhrPatch, Vendor Advisory

Published

Mar 18, 2026

Last Modified

Jun 17, 2026

Status

Analyzed

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