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Fencer Vulns
high 8.1

CVE-2026-31963 json

HTSlib CRAM reader has heap buffer overflow due to improper validation of input

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12930

cvss
8.1
version 3.1, NVD
cisa kev
Not listed
not in CISA's catalog
epss
0.4%
EPSS 0.4% chance of exploitation in 30 days, percentile 30%
public exploits
0
none known

Summary

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.

Patch / fix

  • htslib htslib 1.21.1
  • htslib Debian 14 1.24-2

debian advisories DEBIAN-CVE-2026-31963

Vendor advisories

What the vendors themselves say about their products: affected, fixed or not affected, and what to do.

red hat product security vex CVE-2026-31963 updated cvss 7.3

htslib: HTSlib: Arbitrary code execution via crafted CRAM file

  • Red Hat All currently supported Red Hat products
    not affected: vulnerable code not present

Red Hat CSAF VEX © Red Hat, Inc., from https://security.access.redhat.com/data/csaf/v2/vex/; changed: reduced to product statuses and remediations. CC BY 4.0 · csaf

CISA SSVC

Exploitation
none
Automatable
yes
Technical impact
partial
Assessed
7 mo ago

Exploit prediction

0.37% chance of exploitation in the next 30 days, higher than 30% of all scored CVEs (FIRST EPSS, 2026-11-08).

CVSS scores

assigned by version score vector
CNA 4.0 8.8 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
CNA 4.0 8.8 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/E:X/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X
NVD 3.1 8.1 CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H

Affected products

  • samtools htslib

Classification

Weakness
  • CWE-122 Heap-based Buffer Overflow
  • CWE-129 Improper Validation of Array Index
  • CWE-787 Out-of-bounds Write

References

Sources

Fencer Vulns keeps one entry per vulnerability: the CVE id wins, then GHSA, and records that alias each other are merged, except that two CVEs always keep separate entries. The same data is available as JSON.

CPEs and fixed versions use Anchore's correction of NVD's data: Added CPE configurations because not yet analyzed by NVD.