Out-of-bounds Read in Htslib
CVE-2026-31967
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.
Vulnerability class: Buffer Overflow
EPSS: 0.004 (36.4th percentile) — read the EPSS interpretation.
CVSS v3 metric
CVSS v3 base score 9.1 (Critical). Vector: CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H.
Affected products
- Htslib — versions 1.23
- Samtools Htslib — versions < 1.21.1, >= 1.22, < 1.22.2, = 1.23
Weakness classification (CWE)
References
- security-advisories@github.com (x_refsource_CONFIRM, Patch, Vendor Advisory)
- security-advisories@github.com (Patch, x_refsource_MISC)
Frequently asked questions
- What is CVE-2026-31967?
- CVE-2026-31967 is a critical-severity vulnerability in Htslib, classified under Out-of-bounds Read. CVSS score: 9.1/10. Published 2026-03-18.
- How severe is CVE-2026-31967?
- Critical severity. CVSS v3 base score is 9.1 out of 10.