CVE-2026-31969 HTSlib CRAM decoder has a heap buffer overflow
A heap buffer overflow in HTSlib's CRAM decoder allows attackers to execute arbitrary code or crash the application by tricking users into opening a malicious file.
- Exploited in the wild
- Not known
- Login needed
- Not needed
- Attackable
- Over the internet
- Victim action needed
- A user has to click or open something
- Fix
- Available
What is CVE-2026-31969?
CVE-2026-31969 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, and only if a user opens a file or follows a link.
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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by 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-2026-31969?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31969?
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-2026-31969 being exploited?
There is no known exploitation of CVE-2026-31969 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-2026-31968 HTSlib CRAM decoder vulnerable to buffer overflow
Sources
Also known as DEBIAN-CVE-2026-31969, GHSA-q4cj-f4h5-fqgc, UBUNTU-CVE-2026-31969.