CVE Intelligence
Critical Memory corruption

CVE-2026-31966 — HTSlib CRAM reader has out-of-bounds read due to improper validation of input

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.

Published Mar 18, 2026 · Updated Oct 13, 2026 · Sources: NIST National Vulnerability Database, CVE Program (cve.org) e CISA ADP · CNA: GitHub_M

Who exploits it and how urgent it is

A 0–100 score combining confirmed exploitation, ransomware and APT use, public exploits, EPSS and severity.

No exploitation signal in the sources consulted so far.
How the score was calculated
  • EPSS 0.7% (30-day exploitation probability)+8
  • Technical severity (critical)+10
  • Automatable exploitation (SSVC)+3

The score orders the patch queue; it does not replace your asset context (internet exposure, criticality, compensating controls).

Triage

Is it exploited, how likely is exploitation, what does it touch, and how severe do the sources call it.

Exploitation
Not confirmed
Not in CISA KEV — an absence of record, not proof it is unexploited.
EPSS FIRST
0.65%
ahead of 50% of scored CVEs · Oct 14, 2026
Affects
Htslib
Htslib
CVSS base
9.1
Critical · 3 source(s)

CISA SSVC assessment CISA

Three decision points CISA publishes for the CVEs it assesses (SSVC 2.0.3). A stakeholder decision, not a severity score.

Exploitation
None
none · proof-of-concept · active
Automatable
Yes
can an attacker script the kill-chain steps
Technical impact
Partial
partial · total control of the vulnerable component

Remediation

Fixes and mitigations documented by the sources — linked to the original advisory.

  • Documented patch — github.com (NIST National Vulnerability Database)
  • Documented patch — github.com (NIST National Vulnerability Database)
  • Documented patch — github.com (NIST National Vulnerability Database)
  • Documented patch — github.com (NIST National Vulnerability Database)

First 24 hours

Ordered from the record’s own fields — exposure first, because you cannot patch what you have not found. A rule-generated starting point.

  1. Identify exposed assets running the affected vendor/product/version combinations (Htslib Htslib, Samtools Htslib).
  2. The attack is network-based and needs no privileges: restrict exposure (ACLs, VPN, WAF) until patched.
  3. Apply the fixed version or the patch documented under Remediation.
  4. Search available logs for exploit probes matching the vulnerability class (memory corruption), errors and authentication anomalies.

Affected scope

Vendor, product and versions as the sources word them.

VendorProductVersionsStatusSource
Htslib Htslib < 1.21.1≥ 1.22 and < 1.22.2version 1.23 Vulnerable NIST National Vulnerability Database
Samtools Htslib version < 1.21.1version >= 1.22, < 1.22.2version = 1.23 Vulnerable CVE Program (cve.org) e CISA ADP

Attack characteristics

The CVSS vector, decoded. It describes the attack, not your exposure to it.

Attack vector
Network
Attack complexity
Low
Privileges required
None
User interaction
None
Scope
Unchanged
Confidentiality
High
Integrity
None
Availability
High

Every base score collected

Sources score independently and may disagree; each row says who scored it and under which version.

ScoreVersionSeverityExpl.ImpactScored by
6.9 CVSS 4.0 Medium — — security-advisories@github.com via NIST National Vulnerability Database
6.9 CVSS 4.0 Medium — — GitHub_M via CVE Program (cve.org) e CISA ADP
9.1 CVSS 3.1 Critical 3.9 5.2 nvd@nist.gov via NIST National Vulnerability Database
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:N/A:H (score shown at the top: nvd@nist.gov)

Weakness MITRE

Weakness class according to MITRE’s CWE catalog.

CWE-125 · Out-of-bounds Read

Other CVEs with this weakness →

EPSS over time FIRST

Oct 13, 2026 → Oct 14, 2026 · 2 reading(s) · max 0.65%

Detection

Read off the CVSS vector and the weakness class. Starting points, not tested rules.

  • Prioritize edge telemetry for the network-reachable component (proxy, WAF, IDS/IPS).
  • Correlate service crashes/restarts with inbound traffic; repeated crashes may indicate attempts.
web/proxy/WAF logsnetwork IDS/IPSendpoint telemetry (EDR)crash dumps

Timeline

What happened to this CVE, newest first.

  • 2026
  • Affected products added · samtools/htslib
    Oct 13, 2026 · CVE Program (cve.org) e CISA ADP
  • SSVC assessment updated
    Oct 13, 2026 · CVE Program (cve.org) e CISA ADP
  • Record published
    Oct 13, 2026
  • Fix documented
    Oct 13, 2026 · NIST National Vulnerability Database
  • CVSS changed · 9.1
    Oct 13, 2026 · NIST National Vulnerability Database
  • Source status changed · → Analyzed
    Oct 13, 2026 · NIST National Vulnerability Database
  • Record created in this database
    Oct 13, 2026 · NIST National Vulnerability Database
  • CVE published
    Mar 18, 2026 · GitHub_M

Source activity

Repeated readings are counted rather than listed.

  • 1× Official description updated · Oct 13, 2026 – Oct 13, 2026

References

4 on the record

Elsewhere on this site

Htslib
every CVE for this vendor
Memory corruption
same class
CWE-125
other pages naming this weakness

Related CVEs (same products)

  • CVE-2026-31971 HTSlib CRAM decoder vulnerable to buffer overflow Mar 18, 2026
  • CVE-2026-31967 HTSlib CRAM reader has out-of-bounds read due to improper validation of input Mar 18, 2026
  • CVE-2026-31968 HTSlib CRAM decoder vulnerable to buffer overflow Mar 18, 2026
  • CVE-2026-31969 HTSlib CRAM decoder has a heap buffer overflow Mar 18, 2026
  • CVE-2026-31970 HTSlib BGZF index file reader has a heap buffer overflow Mar 18, 2026
  • CVE-2026-31963 HTSlib CRAM reader has heap buffer overflow due to improper validation of input Mar 18, 2026

Not in any source we poll

Listed rather than left blank: an empty field and an unmeasured one look identical on screen, and only one is a reason to look elsewhere.

  • No confirmed IOCs, IP addresses, domains, file hashes, or malware artifacts supplied.
  • No organization-specific asset inventory, compensating-control status, or patch deployment evidence supplied.
  • No exploit packet captures, log samples, or incident case IDs supplied.

Answered from this record

Text assembled only from the fields above — no additional claims.

What should defenders know first?

CVE-2026-31966 is "HTSlib CRAM reader has out-of-bounds read due to improper validation of input", rated Critical. It affects Htslib (Htslib); versions are in the scope table. It is not in CISA KEV, which does not rule out exploitation. CVSS 9.1 describes technical severity. EPSS 0.65% estimates the probability of exploitation in 30 days; neither replaces your asset context. First verify whether exposed or business-critical assets run the affected versions, apply vendor fixes or mitigations, and preserve logs for review.

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