HTSlib BGZF index file reader has a heap buffer overflow
Key facts
- Attack vector
- Network
- Privileges required
- None
- User interaction
- Passive
- Attack complexity
- Low
- Attack requirements
- None
- Impact type
- —
- Confidentiality · integrity · availability
- None · High · Low
- Fix status
- Fixed
Attack profile from CVSS 4.0 · CNA. Fix status from CNA.
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.
Why it matters now
SSVC decision points
CISA ADP · SSVC 2.0.3
- Exploitation
- None
- Automatable
- No
- Technical impact
- Partial
The decision (Track, Attend, Act) also depends on your mission and well-being impact; see CISA's SSVC guide.
Affected products
| Vendor | Product | Affected versions | Fixed in | Status | Source |
|---|---|---|---|---|---|
| samtools | htslib | before 1.21.1; 1.22 to before 1.22.2; = 1.23 | 1.21.1, 1.22.2 | Patch available | CNA |
- htslib Vendorsamtools Affected before 1.21.1; 1.22 to before 1.22.2; = 1.23 Fixed in 1.21.1, 1.22.2 Patch available CNA
Remediation
- Fix · CNA htslib (samtools) Fixed in 1.21.1, 1.22.2
Vendor assessments
Timeline
- 2026-10-02 Threatist record created from CVE-2026-31970
- 2026-10-16 EPSS moved to the 50th–90th percentile
- 2026-10-25 EPSS moved to the below the 50th percentile
References
More samtools vulnerabilities
- TI-2022-05532 Creation of Temporary File in Directory with Insecure Permissions CVSS 3.1HIGH 7.8
- TI-2026-24512 HTSlib CRAM decoder vulnerable to buffer overflow CVSS 4.0HIGH 8.8
- TI-2026-24507 HTSlib CRAM reader has heap buffer overflow due to improper validation of input CVSS 4.0HIGH 8.8
- TI-2026-24506 HTSlib CRAM reader has heap buffer overflow due to improper validation of input CVSS 4.0HIGH 8.8
- TI-2026-24516 samtools mpileup has use-after-free leading to an invalid read CVSS 4.0MEDIUM 6.9
- TI-2026-24511 HTSlib CRAM reader has out-of-bounds read due to improper validation of input CVSS 4.0MEDIUM 6.9
Sources
- CVE-2026-31970 · CVE Program
- CVE-2026-31970 · NVD
- FIRST EPSS
- CVE-2026-31970 · Red Hat security data · CC BY 4.0
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