Skip to content
Fencer Vulns
high 8.1

CVE-2026-31968 json

HTSlib CRAM decoder vulnerable to buffer overflow

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12942

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 37%
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 using a variety of encodings and compression methods. For the `VARINT` and `CONST` encodings, incomplete validation of the context in which the encodings were used could result in up to eight bytes being written beyond the end of a heap allocation, or up to eight bytes being written to the location of a one byte variable on the stack, possibly causing the values to adjacent variables to change unexpectedly. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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, 1.22.2, 1.23.1
  • htslib Debian 14 1.24-2

debian advisories DEBIAN-CVE-2026-31968

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-2026-31968 updated cvss 7.3

htslib: HTSlib: Buffer overflow in CRAM decoder

  • 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

0.43% chance of exploitation in the next 30 days, higher than 37% 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-121 Stack-based Buffer Overflow
  • CWE-122 Heap-based Buffer Overflow
  • CWE-787 Out-of-bounds Write
  • CWE-843 Access of Resource Using Incompatible Type

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.