# CVE-2026-31966: HTSlib CRAM reader has out-of-bounds read due to improper validation of input > An out-of-bounds read in HTSlib's CRAM decoder allows attackers to leak memory contents or crash the application via crafted files. - **Severity:** Medium 6.9 (`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`) - **Exploited in the wild:** Not known - **Login needed:** Not needed - **Attackable:** Over the internet - **Victim action needed:** Not needed - **Fix available:** Yes - **Published:** 18 Mar 2026 - **Updated:** 18 Mar 2026 - **Also known as:** DEBIAN-CVE-2026-31966, GHSA-5cj8-mj52-8vp3, UBUNTU-CVE-2026-31966 ## What is CVE-2026-31966? CVE-2026-31966 is a medium-severity vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim. ### Official 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. Weakness: CWE-129 (Improper Validation of Array Index), CWE-125 (Out-of-bounds Read) ## Which versions are affected by CVE-2026-31966? It affects 1 product. Products: Htslib Htslib. ## How do I fix CVE-2026-31966? Upgrade to a fixed version. ## Is CVE-2026-31966 being exploited? There is no known exploitation of CVE-2026-31966 in the wild and no public exploit code. ## Other vulnerabilities in samtools htslib - [CVE-2018-13845](https://insights.sbomify.com/CVE-2018-13845/): Memory corruption in n/a (critical 9.8) - [CVE-2017-1000206](https://insights.sbomify.com/CVE-2017-1000206/): Memory corruption in n/a (critical 9.8) - [CVE-2026-31962](https://insights.sbomify.com/CVE-2026-31962/): HTSlib CRAM reader has heap buffer overflow due to improper validation of input (high 8.8) - [CVE-2026-31963](https://insights.sbomify.com/CVE-2026-31963/): HTSlib CRAM reader has heap buffer overflow due to improper validation of input (high 8.8) - [CVE-2026-31968](https://insights.sbomify.com/CVE-2026-31968/): HTSlib CRAM decoder vulnerable to buffer overflow (high 8.8) ## Fix prompt for AI coding agents ```text Check this codebase for CVE-2026-31966 and fix it if it is affected. What it is: CVE-2026-31966 is a medium-severity vulnerability in samtools htslib, published on 18 Mar 2026. An attacker can exploit it over the internet without logging in, with no action from the victim. Exploitation: There is no known exploitation of CVE-2026-31966 in the wild and no public exploit code. Affected product: samtools htslib. No package-level version data is available, so check the vendor advisory linked from the reference page. Task: 1. Search the dependency manifests and lockfiles (for example package.json, package-lock.json, requirements.txt, poetry.lock, uv.lock, pom.xml, build.gradle, go.mod, Cargo.lock, Gemfile.lock) and any Dockerfiles for the affected packages, including transitive dependencies. 2. If an affected version is in use, upgrade it to the fixed version for its release line with the project's package manager, so the lockfile is regenerated. Prefer the smallest upgrade that fixes it. 3. If there is no fix, or the upgrade would break the build, do not guess: explain the risk and the safest workaround instead. 4. Run the tests and summarise what changed and why. 5. If nothing in the project is affected, say so and change nothing. Reference: https://insights.sbomify.com/CVE-2026-31966/ (Markdown: https://insights.sbomify.com/CVE-2026-31966/index.md) ``` ## Sources - CVE record: https://www.cve.org/CVERecord?id=CVE-2026-31966 - NVD: https://nvd.nist.gov/vuln/detail/CVE-2026-31966 - OSV: https://osv.dev/vulnerability/CVE-2026-31966 --- From sbomify Insights: https://insights.sbomify.com/CVE-2026-31966/ Summaries are generated and may contain mistakes; the official description above is the record.