Vulnerability · Published Mar 18, 2026 · Assigned by GitHub_M
CVE-2026-31964HTSlib CRAM decoder has a NULL Pointer Dereference
Medium 6.9
In plain English
A medium-severity null pointer dereference in htslib from samtools. There are no confirmed reports of exploitation so far. The chance it is exploited in the next 30 days is estimated at 0.3% (higher than 28% of all known vulnerabilities). Fixed versions are available - upgrade the affected package.
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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.
Affected packages & fixed versions
| Ecosystem | Package | Fixed in | Advisory |
|---|---|---|---|
| Debian:12 | htslib | no fix listed | DEBIAN-CVE-2026-31964 |
| Debian:13 | htslib | no fix listed | DEBIAN-CVE-2026-31964 |
| Debian:14 | htslib | 1.24-2 | DEBIAN-CVE-2026-31964 |
| Ubuntu:22.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31964 |
| Ubuntu:24.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31964 |
| Ubuntu:25.10 | htslib | no fix listed | UBUNTU-CVE-2026-31964 |
| Ubuntu:26.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31964 |
| Ubuntu:26.10 | htslib | no fix listed | UBUNTU-CVE-2026-31964 |
Affected products (as reported)
Weakness: CWE-476 · Vector: CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N