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Fencer Vulns
high 8.8

CVE-2026-31962 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-2026-12923

cvss
8.8
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 32%
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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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, 1.22.2, 1.23.1
  • htslib Debian 14 1.24-2

debian advisories DEBIAN-CVE-2026-31962

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-2026-31962 updated cvss 7.3

htslib: htslib: Heap buffer overflow leading to 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

0.38% chance of exploitation in the next 30 days, higher than 32% 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:L/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:L/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 8.8 CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Affected products

  • samtools htslib

Classification

Weakness

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.