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Fencer Vulns
high 8.1

CVE-2026-31970 json

HTSlib BGZF index file reader has a heap buffer overflow

published 2026-03-18 7 mo ago modified 2026-06-17 4 mo ago also EUVD-2026-12946

cvss
8.1
version 3.1, NVD
cisa kev
Not listed
not in CISA's catalog
epss
0.5%
EPSS 0.5% chance of exploitation in 30 days, percentile 41%
public exploits
0
none known

Summary

HTSlib is a library for reading and writing bioinformatics file formats. GZI files are used to index block-compressed GZIP [BGZF] files. In the GZI loading function, `bgzf_index_load_hfile()`, it was possible to trigger an integer overflow, leading to an under- or zero-sized buffer being allocated to store the index. Sixteen zero bytes would then be written to this buffer, and, depending on the result of the overflow the rest of the file may also be loaded into the buffer as well. If the function did attempt to load the data, it would eventually fail due to not reading the expected number of records, and then try to free the overflowed 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. The easiest work-around is to discard any `.gzi` index files from untrusted sources, and use the `bgzip -r` option to recreate them.

Patch / fix

  • htslib htslib 1.21.1, 1.22.2, 1.23.1
  • htslib Debian 14 1.24-2

debian advisories DEBIAN-CVE-2026-31970

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-2026-31970 updated cvss 7.3

htslib: HTSlib: BGZF index file reader 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

0.48% chance of exploitation in the next 30 days, higher than 41% 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
  • CWE-122 Heap-based Buffer Overflow
  • CWE-131 Incorrect Calculation of Buffer Size
  • CWE-190 Integer Overflow or Wraparound
  • CWE-787 Out-of-bounds Write
  • CWE-1284 Improper Validation of Specified Quantity in Input

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.