CVE-2026-31962
HTSlib CRAM reader has heap buffer overflow 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. While most alignment records store DNA sequence and quality values, the format also allows them to omit this data in certain cases to save space. Due to some quirks of the CRAM format, it is necessary to handle these records carefully as they will actually store data that needs to be consumed and then discarded. Unfortunately the `cram_decode_seq()` did not handle this correctly in some cases. Where this happened it could result in reading a single byte from beyond the end of a heap allocation, followed by writing a single attacker-controlled byte to the same location. 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. 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 | High8.8 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:H/VA:L/SC:N/SI:N/SA:N |
| NVDNVD · Analyzed | 4.0 | High8.8 | CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/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 (exploitation in 30 days)
- 0.38% · top 67% 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: High 8.8.
Weakness
- CWE-122: Heap-based Buffer Overflow (opens in a new tab)All about CWE-122 and its CVEs
- CWE-125: Out-of-bounds Read (opens in a new tab)All about CWE-125 and its CVEs
- CWE-129: Improper Validation of Array Index (opens in a new tab)All about CWE-129 and its CVEs
- CWE-787: Out-of-bounds Write (opens in a new tab)All about CWE-787 and its CVEs
Affected products
References (2)
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-2026-31962)Record last updated .