CVE-2026-31967 HTSlib CRAM reader has out-of-bounds read due to improper validation of input

Medium 6.9 Published 18 Mar 2026 Updated 18 Mar 2026

An out-of-bounds read in HTSlib's CRAM decoder allows attackers to leak program state or cause crashes via malformed input.

Exploited in the wild: Not known
Login needed: Not needed
Attackable: Over the internet
Victim action needed: Not needed
Fix: Available

What is CVE-2026-31967?

CVE-2026-31967 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, the value of the mate reference id field was not validated. Later use of this value, for example when converting the data to SAM format, could result in the out of bounds array reads when looking up the corresponding reference name. If the array value obtained also happened to be a valid pointer, it would be interpreted as a string and an attempt would be made to write the data as part of the SAM record. 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.

Weakness: CWE-129, CWE-125

Which versions are affected by CVE-2026-31967?

It affects 1 product.

Products include Htslib Htslib.

How do I fix CVE-2026-31967?

Upgrade to a fixed version.

Is CVE-2026-31967 being exploited?

There is no known exploitation of CVE-2026-31967 in the wild and no public exploit code.

Sources

Also known as DEBIAN-CVE-2026-31967, GHSA-33x5-c6vj-8f2w, UBUNTU-CVE-2026-31967.