CVE-2026-31965 HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
An attacker can trigger out-of-bounds reads in HTSlib's CRAM decoder, potentially leaking memory or causing a crash.
- Exploited in the wild
- Not known
- Login needed
- Not needed
- Attackable
- Over the internet
- Victim action needed
- Not needed
- Fix
- Available
What is CVE-2026-31965?
CVE-2026-31965 is a medium-severity 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. 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.
Which versions are affected by CVE-2026-31965?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31965?
Upgrade to a fixed version.
Is CVE-2026-31965 being exploited?
There is no known exploitation of CVE-2026-31965 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-2026-31965, GHSA-mqm2-v645-3qhr, UBUNTU-CVE-2026-31965.