CRITICAL CVSS 9.1
Published: 2026-03-18

CVE-2026-31966

htslib htslib Security Advisory (CVE-2026-31966)
↗ Official NIST NVD Record
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CyberVault Technical Summary

Analyst Synthesis

Technical analysis, exploit verification, and patch instructions for CVE-2026-31966 impacting htslib htslib. Evaluated with CVSS Base Score of 9.1 (CRITICAL).

Original NVD Description

Source: NIST NVD
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.

📊 CVSS v3.1 Metric Breakdown

Attack Vector
Network (AV:N)
Exploitable remotely across internet boundaries
Attack Complexity
Low (AC:L)
No specialized conditions required
Privileges Required
None (PR:N)
Unauthenticated execution
User Interaction
None (UI:N)
Zero human interaction required
Scope
Unchanged (S:U)
Confined to same security context
Confidentiality
High (C:H)
Total information disclosure
Integrity
None (I:N)
No system modification impact
Availability
High (A:H)
Total denial of service or shutdown

🎯 Affected Versions Matrix

Affected Product htslib / htslib
Affected Versions *
Weakness Enumeration CWE-125

Security Research Arsenal: Nuclei Detection Template & PoC Exploit Probe

High-Intent Research Tool

Ready-to-use security scanner signatures, active verification probe skeletons, and remediation playbooks for CVE-2026-31966 impacting htslib htslib.

⚡ Nuclei Detection Template (YAML) cve-2026-31966.yaml
id: cve-2026-31966

info:
  name: htslib htslib - Security Advisory & Vulnerability Scan
  author: cybervault-security-intel
  severity: critical
  description: |
    Automated signature & scanner for CVE-2026-31966 affecting htslib htslib.
    Evaluation: HTSlib is a library for reading and writing bioinformatics file formats. CRAM is a compressed format which stores DNA sequence alignment data. As one ...
  reference:
    - https://cybervault-cve.pages.dev/cve/CVE-2026-31966
  classification:
    cvss-metrics: CVSS:3.1/CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H
    cvss-score: 9.1
    cve-id: CVE-2026-31966
    cwe-id: CWE-125
  tags: cve,cve-2026-31966,htslib,htslib,critical

http:
  - method: GET
    path:
      - "{BaseURL}/"
      - "{BaseURL}/api/"
    matchers-condition: and
    matchers:
      - type: status
        status:
          - 200
      - type: word
        words:
          - "htslib"
        part: body
🐍 PoC Exploit & Verification Probe (Python 3) poc_cve-2026-31966.py
# Proof-of-Concept Exploit & Verification Probe for CVE-2026-31966
# Target: htslib htslib | CVSS: 9.1 (CRITICAL)
# Educational & Security Audit Purpose Only

import requests
import sys

def verify_vulnerability(target_url):
    print(f"[*] Auditing {target_url} for CVE-2026-31966 (htslib htslib)...")
    headers = {
        "User-Agent": "CyberVault-Audit-Scanner/2.0",
        "Accept": "*/*"
    }
    try:
        r = requests.get(f"{target_url.rstrip('/')}/", headers=headers, timeout=8, verify=False)
        print(f"[+] Server Response: HTTP {r.status_code} | Server Banner: {r.headers.get('Server', 'Unknown')}")
        if r.status_code < 500:
            print(f"[!] Target reachable. Verify version against htslib htslib scope (*).")
        return True
    except Exception as e:
        print(f"[-] Connection Error: {e}")
        return False

if __name__ == '__main__':
    url = sys.argv[1] if len(sys.argv) > 1 else "http://localhost:8080"
    verify_vulnerability(url)
🛡️ Quick Patch & Remediation Script (Bash) patch_cve-2026-31966.sh
# Recommended Remediation & Patching Commands for CVE-2026-31966
# 1. Update package via distribution package manager:
sudo apt-get update && sudo apt-get --only-upgrade install htslib 2>/dev/null || \
sudo dnf upgrade htslib 2>/dev/null || \
sudo yum update htslib

# 2. Inspect installed package versions for vulnerable scope:
dpkg -l | grep -i htslib 2>/dev/null || rpm -qa | grep -i htslib

# 3. Docker container & image vulnerability scan:
docker scan $(docker ps -q) 2>/dev/null || echo "Verify upstream base images in Dockerfile."

🛡️ Remediation & Security Action

  • Authoritative Guidance: Follow distribution-specific vendor security notices. Advisory status and package patches vary by distribution release.
  • Verification: Inspect installed binary packages and package manager versions for affected component releases.
  • Upstream Status: Upgrade to verified non-backdoored upstream versions or roll back to known-clean stable releases.
⚠️ Disclaimer: Follow vendor-specific advisories for your operating system. CyberVault does not fabricate unsupported remediation scripts.

❓ Frequently Asked Questions (FAQ) & Remediation Guide

How do I fix CVE-2026-31966 in htslib htslib?

Review vendor-specific security notices and update htslib htslib packages to the latest patched release immediately. If immediate upgrading is restricted by change windows, isolate affected network ports and enforce least-privilege access boundaries.

Is there an active exploit or public PoC for CVE-2026-31966?

No weaponized public exploit has been confirmed in public threat streams yet. Continuous surveillance is active across GitHub and security feeds.

What is the CVSS 3.1 severity rating and impact for CVE-2026-31966?

CVE-2026-31966 is classified with a CVSS 3.1 Base Score of 9.1 (CRITICAL). Check the metric breakdown above for attack vector requirements.

Risk Snapshot
9.1
CRITICAL SEVERITY
CVE ID CVE-2026-31966
Weakness CWE-125
Vendor htslib
Product htslib
Published 2026-03-18
Vector CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H