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Vulnerabilities

Vulnerability · CVE-2026-31963

HTSlib is a library for reading and writing bioinformatics file formats.

Published Mar 18, 2026 · catalog updated Jun 17, 2026 · htslib htslib

Severity
High8.8
Known exploitation
Not in CISA/VulnCheck KEV
EPSS
0.5%
Remediation
Advisory link
Affected products
cpe htslib/htslib

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 these features, an out-by-one error in a test for CRAM features that appear beyond the extent of the CRAM record sequence could result in an invalid write of one attacker-controlled byte beyond the end of a heap buffer. 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 analysis

Mechanism and impact are interpreted from ingested advisories — not independent exploit research.

How to fix CVE-2026-31963

What to do

Three reads of the same public record: the decision, the versions on file, and the signals. Confirm the vendor advisory before you patch. This page does not publish exploit steps.

Executive

This is a public record, not a confirmed incident. CVE-2026-31963 is a high issue in htslib htslib (CVSS 8.8). CISA does not currently list it as known exploited. Next step: Compare installed versions with the linked vendor advisory before changing production.

System administrator

Check whether htslib htslib is installed. Ranges on record: htslib/htslib; htslib/htslib (1.23). Compare installed versions with the linked vendor advisory before changing production.

Security analyst

CVSS 8.8. EPSS 0.5%. CISA does not currently list it as known exploited. Weaknesses: CWE-122, CWE-129, CWE-787. Sources: cve_org, epss, nvd. Exploit links, when listed below, point at the original publisher.

Related intelligence

  • Exploitation evidence

    Not listed as known exploited in CISA KEV. Not in CISA KEV or VulnCheck KEV.

  • 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.

  1. 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. 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 a

  2. 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. 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 a

Affected versions

Enter an installed version to get a verified affected / not-affected result against the ranges below.

  • cpe htslib/htslibversion unspecified
  • cpe htslib/htslib1.23

Sources

  • CVE.orgVulnerability recordCVE-2026-31963

    Official CVE identifier

    cve.org
  • FIRST EPSSExploitation probabilityCVE-2026-31963

    30-day exploitation probability 0.5%

    first.org
  • NIST NVDVulnerability recordCVE-2026-31963

    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 ali

    nvd.nist.gov

References

Freshness

Last verified in this catalog Oct 18, 2026. Significant claims (KEV, EPSS, CVSS, affected ranges) come from the source rows above — open the original publisher for the authoritative advisory.