HTSlib CRAM reader has out-of-bounds read due to improper validation of input
Key facts
- Attack vector
- Network
- Privileges required
- None
- User interaction
- None
- Attack complexity
- Low
- Attack requirements
- None
- Impact type
- —
- Confidentiality · integrity · availability
- Low · None · 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. As one method of removing redundant data, CRAM uses reference-based compression so that instead of storing the full sequence for each alignment record it stores a location in an external reference sequence along with a list of differences to the reference at that location as a sequence of "features". When decoding CRAM records, the reference data is stored in a char array, and parts matching the alignment record sequence are copied over as necessary. Due to insufficient validation of the feature data series, it was possible to make the `cram_decode_seq()` function copy data from either before the start, or after the end of the stored reference either into the buffer used to store the output sequence for the cram record, or into the buffer used to build the SAM `MD` tag. This allowed arbitrary data to be leaked to the calling function. This bug may allow information about program state to be leaked. It may also cause a program crash through an attempt to access invalid memory. 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
- Yes
- 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-2026-31966
- 2026-10-14 EPSS moved to the 50th–90th percentile
- 2026-10-25 EPSS moved to the below the 50th percentile
References
Patch 4
- https://github.com/samtools/htslib/security/advisories/GHSA-5cj8-mj52-8vp3
- https://github.com/samtools/htslib/commit/22ec5230ef95769ab009420da69568c7e530af28
- https://github.com/samtools/htslib/commit/2a45eb129d703ad27f9fabc8169f0e94d3c69fa3
- https://github.com/samtools/htslib/commit/4a5ef25eb1fb3d64438103316fffe423b2c3f5f4
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-2026-31966 · CVE Program
- CVE-2026-31966 · NVD
- FIRST EPSS
- CVE-2026-31966 · Red Hat security data · CC BY 4.0
This product uses the NVD API but is not endorsed or certified by the NVD. Sources and licences