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Fencer Vulns
high 8.1

CVE-2026-31969 json

HTSlib CRAM decoder has a heap buffer overflow

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12944

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 29%
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. When reading data encoded using the `BYTE_ARRAY_STOP` method, an out-by-one error in the `cram_byte_array_stop_decode_char()` function check for a full output buffer could result in a single attacker-controlled byte being written beyond the end of a heap allocation. 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-2026-31969

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-2026-31969 updated cvss 7.3

htslib: HTSlib: CRAM decoder has a heap buffer overflow

  • 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
no
Technical impact
partial
Assessed
7 mo ago

Exploit prediction

0.36% chance of exploitation in the next 30 days, higher than 29% of all scored CVEs (FIRST EPSS, 2026-11-08).

CVSS scores

assigned by version score vector
CNA 4.0 7.1 CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:H/VA:L/SC:N/SI:N/SA:N
CNA 4.0 7.1 CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/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

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.