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Fencer Vulns
high 7.5

CVE-2026-31964 json

HTSlib CRAM decoder has a NULL Pointer Dereference

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12932

cvss
7.5
version 3.1, NVD
cisa kev
Not listed
not in CISA's catalog
epss
0.3%
EPSS 0.3% chance of exploitation in 30 days, percentile 27%
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. 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 `CONST`, `XPACK` and `XRLE` encodings did not properly implement the interface needed to do this. Trying to decode records with omitted sequence or quality data using these encodings would result in an attempt to write to a NULL pointer. Exploiting this bug causes a NULL pointer dereference. Typically this will cause the program to crash. 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-2026-31964

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-2026-31964 updated cvss 5.0

htslib: HTSlib: Denial of Service via NULL pointer dereference in CRAM decoding

  • 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

0.34% chance of exploitation in the next 30 days, higher than 27% of all scored CVEs (FIRST EPSS, 2026-11-08).

CVSS scores

assigned by version score vector
CNA 4.0 6.9 CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/VA:L/SC:N/SI:N/SA:N
CNA 4.0 6.9 CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:N/VI:L/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 7.5 CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/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.