CVE-2026-31968 HTSlib CRAM decoder vulnerable to buffer overflow
A buffer overflow in HTSlib's CRAM decoder allows attackers to execute arbitrary code or crash applications by tricking users into opening malicious files.
- Exploited in the wild
- Not known
- Login needed
- Not needed
- Attackable
- Over the internet
- Victim action needed
- Not needed
- Fix
- Available
What is CVE-2026-31968?
CVE-2026-31968 is a high-severity memory corruption vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim.
Official 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. 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.
Which versions are affected by CVE-2026-31968?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31968?
Upgrade to a fixed version.
Upgrade to the fixed version. Memory-safe languages, compiler hardening and fuzzing prevent most new cases. More about Memory corruption.
Is CVE-2026-31968 being exploited?
There is no known exploitation of CVE-2026-31968 in the wild and no public exploit code.
Other vulnerabilities in samtools htslib
- CVE-2018-13845 Memory corruption in n/a
- CVE-2017-1000206 Memory corruption in n/a
- CVE-2026-31962 HTSlib CRAM reader has heap buffer overflow due to improper validation of input
- CVE-2026-31963 HTSlib CRAM reader has heap buffer overflow due to improper validation of input
- CVE-2020-36403 Memory corruption in n/a
Sources
Also known as DEBIAN-CVE-2026-31968, GHSA-cgcm-c9r2-p57j, UBUNTU-CVE-2026-31968.