High 8.8Published Mar 18, 2026

CVE-2026-31963HTSlib CRAM reader has heap buffer overflow due to improper validation of input

Updated under an hour ago (Oct 26, 2026, 1:40 PM ET)

Does this affect you?

It affects samtools htslib and 1 other product. Add what you run to find out whether that includes you.

No exploitation reported and no EPSS estimate yet.

Do this next

Start free and add your stack

Free account, 1 product

Every CVE for samtools htslib

Exploited in the last 30 days

HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. Exploiting this bug causes a heap buffer overflow. If a user opens a file crafted to exploit this issue, it could lead to the program crashing, or overwriting of data and heap structures in ways not expected by the program. It may be possible to use this to obtain arbitrary code execution. Versions 1.23.1, 1.22.2 and 1.21.1 include fixes for this issue. There is no workaround for this issue.

CVSS: 8.8 HIGH (v4.0, CNA)CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
Weakness (CWE): CWE-122, CWE-129, CWE-787
Known exploited: Not in CISA's KEV catalog
EPSS (exploitation in the next 30 days): Not loaded for this CVE
Assigned by: GitHub_M
NVD analysis: Analyzed
Record last updated: Mar 18, 2026
First seen by InfoSec Signals: Oct 9, 2026

Affected products

Affected products

samtools htslib samtools:htslib (from the name)	before 1.21.1; from 1.22, < 1.22.2; = 1.23	CNA record
htslib htslib htslib:htslib	before 1.21.1; from 1.22 before 1.22.2; 1.23	NVD

References

References

https://github.com/samtools/htslib/security/advisories/GHSA-qgqh-h2q9-7w3c	x-refsource-confirm, patch, vendor-advisory
https://github.com/samtools/htslib/commit/8bcc9907be0f945ddc31796d64f078fa05456acd	x-refsource-misc, patch

The CVE record on cve.org NVD's entry

The CVE record is authoritative. Products marked “from the name” were identified from the CNA's free-text names, not a CPE, and are matched less certainly. This product uses the NVD API but is not endorsed or certified by the NVD.