CVE-2026-31966
HTSlib CRAM reader has out-of-bounds read due to improper validation of input
- Published
- Updated
- Reserved
- Assigned by
- GitHub_M
Description
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.
Timeline
ID reserved
By GitHub_M
- 8 days later
· 8 days later
Published
Changes after publication (a new score, a public exploit, EPSS crossing 1, 10 or 50 %, leaving KEV) are kept since November 2026; earlier ones are not known.
Scores
| Scored by | CVSS | Score | Vector |
|---|---|---|---|
| GitHub_MCNA (assigner) | 4.0 | Medium6.9 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/VA:L/SC:N/SI:N/SA:N |
| NVDNVD · Analyzed | 4.0 | Medium6.9 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:N/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 (exploitation in 30 days)
- 0.55% · top 54% of all CVEs (7 Nov 2026)
- CISA SSVC
- Exploitation: none · Automatable: yes · Technical impact: partial
The list uses the assigner's score when there is one, then CISA's, then NVD's: Medium 6.9.
Weakness
Affected products
References (4)
- https://github.com/samtools/htslib/security/advisories/GHSA-5cj8-mj52-8vp3 (opens in a new tab)x_refsource_CONFIRM
- https://github.com/samtools/htslib/commit/22ec5230ef95769ab009420da69568c7e530af28 (opens in a new tab)x_refsource_MISC
- https://github.com/samtools/htslib/commit/2a45eb129d703ad27f9fabc8169f0e94d3c69fa3 (opens in a new tab)x_refsource_MISC
- https://github.com/samtools/htslib/commit/4a5ef25eb1fb3d64438103316fffe423b2c3f5f4 (opens in a new tab)x_refsource_MISC
Sources
The same CVE in the primary databases and aggregators, to check against.
- CVE.org record (opens in a new tab)
- CVE List JSON (GitHub) (opens in a new tab)
- NVD (opens in a new tab)
- FIRST EPSS (opens in a new tab)
- OSV.dev (opens in a new tab)
- GitHub Advisories (opens in a new tab)
- CIRCL Vulnerability-Lookup (opens in a new tab)
Badge for a README or a ticket
[](https://trackcve.app/cve/CVE-2026-31966)Record last updated .