CVE-2026-31970: 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 l...

Description

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.

Metrics

CVSS 3.1

8.1/10

CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:H/A:H

CVSS 4.0

7.1/10

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

EPSS Probability

0.45%

36.0th percentile

Probability of exploitation in the next 30 days. Learn more

Weakness Enumeration

Affected Software

Vendor	Product	Versions
Htslib	Htslib	< 1.21
Htslib	Htslib	>= 1.22, < 1.22.2
Htslib	Htslib	1.23

References

https://github.com/samtools/htslib/commit/6dd0d7d0e9e7e2e173a28969e624db8bc8bb5828Patch
https://github.com/samtools/htslib/security/advisories/GHSA-p345-84hx-fq6qMitigation, Patch, Vendor Advisory
http://www.openwall.com/lists/oss-security/2026/03/18/9Mailing List, Third Party Advisory

Timeline

Published: Mar 18, 2026
Last Modified: Jun 17, 2026
Status: Analyzed

Frequently Asked Questions

What is CVE-2026-31970?

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.

How severe is CVE-2026-31970?

CVE-2026-31970 has a CVSS score of 7.1/10 (HIGH severity). The EPSS model estimates a 0.45% probability of exploitation in the next 30 days.

How do I fix CVE-2026-31970?

Check the vendor references and advisories linked above for patched versions and mitigation guidance. You can also run a Strix scan to test if your systems are affected.