HTSlib CRAM decoder vulnerable to 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. 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_LEN` method, the `cram_byte_array_len_decode()` failed to validate that the amount of data being unpacked matched the size of the output buffer where it was to be stored. Depending on the data series being read, this could result either in a heap or a stack overflow with attacker-controlled bytes. Depending on the data stream this could result either in a heap buffer overflow or a stack overflow. If a user opens a file crafted to exploit this issue it could lead to the program crashing, overwriting of data structures on the heap or stack in ways not expected by the program, or changing the control flow of 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.
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-2026-31971
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-2026-31971 · CVE Program
- CVE-2026-31971 · NVD
- FIRST EPSS
- CVE-2026-31971 · Red Hat security data · CC BY 4.0
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