CVE-2026-31962
Official description Straight from the sourceThe vendor's or NVD's own wording, published unedited. Authoritative, but often terse — it says what broke, rarely what to do.
NVD · uneditedHTSlib 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.
Technical summary Written by usOur analysis, written from the advisory, the CVSS vector and the affected-version data. It adds context the advisory leaves out, and never invents facts that are not in the source.
dbcve analysisData overflows a buffer allocated on the heap, corrupting neighbouring heap structures and allocator metadata that a patient attacker can groom into control of execution. It is subtler than a stack overflow but just as dangerous. The fix is validating lengths before every write and using safe allocators and bounded operations.
General guidance for the heap-based buffer overflow class — the official description and references above are authoritative for this specific CVE. Want a bespoke review and a reviewed fix? Ask our team →
Affected products & versions What the vendor confirmedThe version ranges the vendor confirmed as vulnerable. If your version sits inside a range here, treat yourself as exposed until you have upgraded.
NVD · CPE data< 1.21.1>= 1.22, < 1.22.2= 1.23CVSS breakdown How the score is builtThe industry scoring standard. It rates how the flaw is reached, what it takes to exploit, and what an attacker gains — the score is derived from those, not the other way round.
From the vector- Attack vector
- Network
- Complexity
- Low
- Privileges
- None
- User interaction
- Required
- Scope
- Unchanged
- Confidentiality
- High
- Integrity
- High
- Availability
- High
CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H
Remediation Closing itWhat it takes to close this. Where a vendor fix exists we point at it; where none exists we say so plainly, and can build one. Effort estimates are scoped from the advisory, not from your codebase.
dbcve · scoped1.21.11.22.2
Upgrade to htslib 1.21.1, 1.22.2, or 1.23.1 (whichever corresponds to your current major version branch; 1.23.1 is the latest stable release)
- 1. Identify the current htslib version in use by checking your project's dependencies or running `htslib --version` if available
- 2. Determine which major version branch you are currently on (1.21.x, 1.22.x, or 1.23.x)
- 3. For version 1.21.x systems: upgrade to version 1.21.1
- 4. For version 1.22.x systems: upgrade to version 1.22.2
- 5. For version 1.23.x systems: upgrade to version 1.23.1
- 6. If using a package manager (e.g., apt, yum, brew, conda), update the package: `apt-get update && apt-get install libhts-dev` or `conda install htslib` or corresponding command for your package manager
- 7. If building from source, download the new version from https://github.com/samtools/htslib/releases and rebuild
- 8. Rebuild any dependent applications that link against htslib
Generated from the published advisory — verify against the referenced sources before acting.
Scan for this in your stack
Free · runs locallyCheck whether your project pulls in CVE-2026-31962 — or any other known-vulnerable package — straight from your lock files. Free and open source; it runs locally and uploads nothing.
References Go to the primary sourcePrimary sources — vendor advisories, patches and trackers. Where our summary and a reference disagree, the reference wins.
Primary sourcesPractitioner notes
ContributedPeer-ranked notes from engineers who’ve handled CVE-2026-31962 in production — separate from our analysis above.
The advisory tells you what broke. It rarely tells you what actually worked. If you’ve dealt with this one, that detail is what the next engineer is searching for.
- The version that genuinely resolved it — not the one the vendor claimed
- A config change or rule that shut the vector down
- A gotcha in the upgrade path that cost you an afternoon
No notes yet
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- Version or environment caveats, and links to real fixes
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