Vulnerability · CVE-2026-31962
HTSlib is a library for reading and writing bioinformatics file formats.
Published Mar 18, 2026 · corrected/updated Jun 17, 2026 · htslib htslib · evidence confidence high
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 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.
Grounded briefings
Catalog interpretations for three audiences. Each brief cites ingested metadata and the original advisories below. They are not independent research and they do not invent exploit steps.
Executive
CVE-2026-31962 is a high public vulnerability record for htslib htslib. It is not currently listed in the CISA Known Exploited catalog. Check the linked vendor or CERT advisories for patch status. This summary is a catalog interpretation of the ingested metadata and cites the original advisories below.
System administrator
Identify whether htslib htslib is in your estate, then compare installed versions with the affected ranges. Affected packages or ranges on record: htslib/htslib; htslib/htslib (1.23). Check the linked vendor or CERT advisories for patch status. Prefer the vendor or distribution advisory linked in Sources before changing production systems. This is a catalog interpretation, not a runbook.
Security analyst
Signals on file: CVSS 8.8 (technical impact); EPSS 0.6% (30-day exploitation probability). It is not currently listed in the CISA Known Exploited catalog. Weakness classes: CWE-122, CWE-125, CWE-129, CWE-787. Sources contributing to this record: cve_org, epss, nvd. Public exploit references, when present, are outbound links only and are not proof of active exploitation. This is a catalog interpretation of stored metadata.
Exploitation and remediation
Exploitation evidence
Not listed as known exploited in CISA KEV. Not in CISA KEV or VulnCheck KEV.
Patch and remediation
A patch or advisory reference is linked. Open the original publisher for availability by product version.
Safe detection guidance
Compare installed versions with the affected ranges below and verify the advisory from the original publisher. This site stores metadata and outbound links only; it does not ship exploit code or proof-of-concept payloads.
Code
The project this record applies to. Exploit listings stay in References.
Timeline
Detection, updates, and resolution for this record.
Mar 18, 2026 · NIST NVD
Detected
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
Jun 17, 2026 · NIST NVD
Updated
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
Affected
- cpe htslib/htslibversion unspecified
- cpe htslib/htslib1.23
Sources
- CVE.orgVulnerability recordCVE-2026-31962
Official CVE identifier
cve.org - FIRST EPSSExploitation probabilityCVE-2026-31962
30-day exploitation probability 0.6%
first.org - NIST NVDVulnerability recordCVE-2026-31962
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 sav
nvd.nist.gov