EUVD-2026-12923
CVSS Vector
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
Lifecycle Timeline
4Description
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.
Analysis
HTSlib versions prior to 1.23.1, 1.22.2, and 1.21.1 contain a heap buffer overflow vulnerability in the cram_decode_seq() function when processing CRAM-formatted bioinformatics files with omitted sequence and quality data. An attacker can craft a malicious CRAM file that triggers an out-of-bounds read followed by an attacker-controlled single-byte write to heap memory, potentially enabling arbitrary code execution, data corruption, or denial of service when a user opens the file. …
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Remediation
Within 7 days: Identify all affected systems and apply vendor patches promptly. If patching is delayed, consider network segmentation to limit exposure.
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Priority Score
Vendor Status
Debian
| Release | Status | Fixed Version | Urgency |
|---|---|---|---|
| bullseye | vulnerable | 1.11-4 | - |
| bookworm | vulnerable | 1.16+ds-3 | - |
| trixie | vulnerable | 1.21+ds-1 | - |
| forky, sid | vulnerable | 1.22.1+ds2-1 | - |
| (unstable) | fixed | (unfixed) | - |
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External POC / Exploit Code
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