CVE-2026-31971
What it is
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.
At a glance
- Exploitability
- Can be exploited over the network without logging in, but needs a user to act. High risk of data tampering.
- Exploit odds
- 0.4% chance of exploitation in the next 30 days (EPSS).
- Fix
- A patch, advisory or fixed version is referenced. Upgrade or apply it.
Timeline
- PublishedDisclosed publicly on CVE.org and NVD
- Last updatedMost recent change to the record
Why it ranks here
- Exploited in the wild: no, CISA does not list it.
- Exploit odds: 0.4% in the next 30 days (EPSS).
- Severity: 7.1 HIGH (CVSS).
- Fix: a patch or advisory is linked.
Details
- Published
- Last modified
- Exploit probability
- 0.4% · EPSS, next 30 days
- Weakness
- CWE-121
- Record status
- Analyzed
Affected
- Htslib < 1.21.1
- Htslib < 1.22.2
- Htslib 1.23
Attack profile CVSS 4.0 · 7.1
- Attack vector
- Network
- Complexity
- Low
- Attack requirements
- None
- Privileges needed
- None
- User interaction
- Passive
- Confidentiality
- None
- Integrity
- High
- Availability
- Low
Raw vector
CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/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
Is it in your code?
Hand this to your coding agent. It searches your project for the affected products and checks versions. Nothing leaves your machine.
Read https://cve-list.com/agent/cve/CVE-2026-31971.md and follow it. Check whether this project is affected by CVE-2026-31971. Read only. Don't change anything and don't upload my code. Tell me yes, no or not sure, with the file as proof.
Fix and advisories
- https://github.com/samtools/htslib/commit/01cd003b46fa2ebea4d9be5475b11217eb4c11be
- https://github.com/samtools/htslib/security/advisories/GHSA-jvx4-4wq7-6fmh