Vulnerability · Published Mar 18, 2026 · Assigned by GitHub_M
CVE-2026-31967HTSlib CRAM reader has out-of-bounds read 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 0.5% (higher than 41% 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, 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.
Affected packages & fixed versions
| Ecosystem | Package | Fixed in | Advisory |
|---|---|---|---|
| Debian:12 | htslib | no fix listed | DEBIAN-CVE-2026-31967 |
| Debian:13 | htslib | no fix listed | DEBIAN-CVE-2026-31967 |
| Debian:14 | htslib | 1.24-2 | DEBIAN-CVE-2026-31967 |
| Ubuntu:22.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31967 |
| Ubuntu:24.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31967 |
| Ubuntu:25.10 | htslib | no fix listed | UBUNTU-CVE-2026-31967 |
| Ubuntu:26.04:LTS | htslib | no fix listed | UBUNTU-CVE-2026-31967 |
| Ubuntu:26.10 | htslib | no fix listed | UBUNTU-CVE-2026-31967 |
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