CVE-2026-31968

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. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

• CWE-121
• CWE-122
• CWE-787
• CWE-843

• https://github.com/samtools/htslib/commit/0ec436796eca7b4ce7fcc9b77270c102da29bb2ePatch
• https://github.com/samtools/htslib/security/advisories/GHSA-cgcm-c9r2-p57jPatch, Vendor Advisory

Published

Mar 18, 2026

Last Modified

Jun 17, 2026

Status

Analyzed

• How Strix found a critical auth bypass in etcdStrix autonomously discovered a critical authentication bypass in etcd, later designated CVE-2026-33413.
• Autonomous PentestingAI agents that find and validate exploitable vulnerabilities like this one across your applications.
• PR ReviewsPentest every pull request so vulnerable code is caught before it ships to production.
• AI Penetration TestingHow AI-driven penetration testing continuously covers your attack surface.

• CVE-2026-31962HTSlib is a library for reading and writing bioinformatics f…8.8
• CVE-2026-31963HTSlib is a library for reading and writing bioinformatics f…8.1
• CVE-2026-31964HTSlib is a library for reading and writing bioinformatics f…7.5
• CVE-2026-31965HTSlib is a library for reading and writing bioinformatics f…8.2
• CVE-2026-31966HTSlib is a library for reading and writing bioinformatics f…9.1
• CVE-2026-31967HTSlib is a library for reading and writing bioinformatics f…9.1
• CVE-2026-31969HTSlib is a library for reading and writing bioinformatics f…8.1
• CVE-2026-3197Rejected reason: ** REJECT ** DO NOT USE THIS CANDIDATE NUMB…
• CVE-2026-31970HTSlib is a library for reading and writing bioinformatics f…8.1
• CVE-2026-31971HTSlib is a library for reading and writing bioinformatics f…8.1
• CVE-2026-31972SAMtools is a program for reading, manipulating and writing …9.8
• CVE-2026-31973SAMtools is a program for reading, manipulating and writing …7.5