Vulnerability · Published Mar 18, 2026 · Assigned by GitHub_M
CVE-2026-31965HTSlib CRAM reader has out-of-bounds reads due to improper validation of input
Medium 6.9
In plain English
A medium-severity out-of-bounds read 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 0.4% (higher than 34% 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. 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.
Affected packages & fixed versions
| Ecosystem | Package | Fixed in | Advisory |
|---|---|---|---|
| Debian:12 | htslib | no fix listed | DEBIAN-CVE-2026-31965 |
| Debian:13 | htslib | no fix listed | DEBIAN-CVE-2026-31965 |
| Debian:14 | htslib | 1.24-2 | DEBIAN-CVE-2026-31965 |
| Ubuntu:22.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31965 |
| Ubuntu:24.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31965 |
| Ubuntu:25.10 | htslib | no fix listed | UBUNTU-CVE-2026-31965 |
| Ubuntu:26.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31965 |
| Ubuntu:26.10 | htslib | no fix listed | UBUNTU-CVE-2026-31965 |
Affected products (as reported)
Weakness: CWE-125, CWE-129 · Vector: CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N