CVE-2026-31966 HTSlib CRAM reader has out-of-bounds read due to improper validation of input
An out-of-bounds read in HTSlib's CRAM decoder allows attackers to leak memory contents or crash the application via crafted 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-2026-31966?
CVE-2026-31966 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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt 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-2026-31966?
It affects 1 product.
Products include Htslib Htslib.
How do I fix CVE-2026-31966?
Upgrade to a fixed version.
Is CVE-2026-31966 being exploited?
There is no known exploitation of CVE-2026-31966 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-2026-31966, GHSA-5cj8-mj52-8vp3, UBUNTU-CVE-2026-31966.