VulnerabilityPublished 18 Mar 2026

CVE-2026-31966: samtools htslib · Out-of-bounds Read

Affects samtools htslibSource CVE Database V5

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Not known to be exploited · CVSS 6.9 Medium : upgrade to 1.22.2 or 1.21.1 when convenient.

Data as of 29 Oct 2026, 19:04 UTC

CVSS 4.0 base score

6.9Medium

How severe the flaw is on the 0–10 CVSS scale.

EPSS: 0.5% chance of exploitation in 30 days – higher than 45% of CVEsExploit Prediction Scoring System: the likelihood attackers will use this flaw soon.
Patch: Available – fixed in 1.22.2, 1.21.1

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

Attack Vector: Network
Attack Complexity: Low
Attack Requirements: None
Privileges Required: None
User Interaction: None
Vulnerable system confidentiality: Low
Vulnerable system integrity: None
Vulnerable system availability: Low
Subsequent system confidentiality: None
Subsequent system integrity: None
Subsequent system availability: None

Bold values are the worst case: easiest to exploit or largest impact.

Attack Vector: Network: The vulnerable system is bound to the network stack and the set of possible attackers extends beyond the other options listed below, up to and including the entire Internet. Such a vulnerability is often termed “remotely exploitable” and can be thought of as an attack being exploitable at the protocol level one or more network hops away (e.g., across one or more routers).
Attack Complexity: Low: The attacker must take no measurable action to exploit the vulnerability. The attack requires no target-specific circumvention to exploit the vulnerability. An attacker can expect repeatable success against the vulnerable system.
Attack Requirements: None: The successful attack does not depend on the deployment and execution conditions of the vulnerable system. The attacker can expect to be able to reach the vulnerability and execute the exploit under all or most instances of the vulnerability.
Privileges Required: None: The attacker is unauthorized prior to attack, and therefore does not require any access to settings or files of the vulnerable system to carry out an attack.
User Interaction: None: The vulnerable system can be exploited without interaction from any human user, other than the attacker.
Vulnerable system confidentiality: Low: There is some loss of confidentiality. Access to some restricted information is obtained, but the attacker does not have control over what information is obtained, or the amount or kind of loss is limited. The information disclosure does not cause a direct, serious loss to the Vulnerable System.
Vulnerable system integrity: None: There is no loss of integrity within the Vulnerable System.
Vulnerable system availability: Low: Performance is reduced or there are interruptions in resource availability. Even if repeated exploitation of the vulnerability is possible, the attacker does not have the ability to completely deny service to legitimate users. The resources in the Vulnerable System are either partially available all of the time, or fully available only some of the time, but overall there is no direct, serious consequence to the Vulnerable System.
Subsequent system confidentiality: None: There is no loss of confidentiality within the Subsequent System or all confidentiality impact is constrained to the Vulnerable System.
Subsequent system integrity: None: There is no loss of integrity within the Subsequent System or all integrity impact is constrained to the Vulnerable System.
Subsequent system availability: None: There is no impact to availability within the Subsequent System or all availability impact is constrained to the Vulnerable System.

Definitions: FIRST CVSS v4.0 specification.

Exploitation evidence

Disclosed: evidence found.
CVE published 18 Mar 2026
Detectable: no evidence on record.
No public nuclei template indexed
Weaponized: no evidence on record.
No public exploit code indexed in Metasploit or Exploit-DB
Exploited in the wildExploited: no evidence on record.
Not in CISA KEV and no source reports exploitation
Observed by OffSeq MirageSeen by Mirage: no evidence on record.
No attack traffic recorded by OffSeq Mirage sensors

A missing step is not evidence of safety. Sources: cve.org (opens in a new tab), the Metasploit, Exploit-DB and nuclei-templates index as of 29 Oct 2026.

Disclosed: The CVE record is public on cve.org. Its publication is t = 0.
Detectable: A public nuclei template can find exposed instances, for defenders and attackers alike.
Weaponized: A Metasploit exploit module or Exploit-DB entry exists (Metasploit scanner modules do not count), or CISA SSVC or the CVSS exploit maturity reports a public proof of concept.
Exploited in the wild: CISA KEV lists it, CISA SSVC rates exploitation active, or a source reports attacks.
Observed by OffSeq Mirage: OffSeq Mirage honeypot sensors recorded attack traffic for this CVE, or found exposed hosts without attack traffic.

Moments are spaced evenly, not to scale; a dashed line marks a gap of six months or more. Deltas count from t = 0. Sources that give only a date (CISA KEV, Exploit-DB, or a time of exactly 00:00Z) read “same day” rather than hours. Metasploit modules carry the flaw’s disclosure date, not their release date, and nuclei templates carry no date, so both appear above but not on the timeline.

What to do

Upgrade htslib to 1.22.2 or 1.21.1; samtools/htslib to 1.21.1.

Affected software

Product	Affected	Fixed in
samtoolshtslib	Affected <1.21.1 >=1.22 <1.22.2 =1.23	Fixed in 1.22.2 1.21.1
GitHubsamtools/htslib`pkg:github/samtools/htslib`Other threats	Affected <1.21.1 =1.23	Fixed in 1.21.1

Check your own hosts for these packages with threat-finder (opens in a new tab), our free open-source scanner.

AI-suggested

The only effective mitigation is to upgrade htslib to a fixed version: 1.21.1, 1.22.2, or 1.23.1 or later. Organizations should audit their bioinformatics pipelines and tools to identify usage of vulnerable htslib versions and update accordingly. Additionally, implement strict input validation and filtering to ensure only trusted CRAM files are processed, reducing exposure to crafted malicious files. Employ sandboxing or containerization for bioinformatics tools to limit the impact of potential crashes or memory leaks. Monitor logs and application behavior for crashes or anomalies that could indicate exploitation attempts. Since no workaround exists, patch management and supply chain verification are critical. Finally, maintain awareness of updates from samtools and related projects for any further advisories.

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.

Impact

The primary impact of CVE-2026-31966 is the potential leakage of arbitrary memory contents from the vulnerable application processing CRAM files. This could expose sensitive information about the program's internal state or data in memory, which might aid attackers in further exploitation or reconnaissance. Additionally, the out-of-bounds read can cause application crashes, leading to denial of service in bioinformatics pipelines relying on htslib. Since htslib is a foundational library used in many bioinformatics tools and workflows worldwide, this vulnerability could disrupt critical genomic data processing, affecting research, clinical diagnostics, and pharmaceutical development. The lack of authentication or user interaction requirements means that any system processing untrusted CRAM files is at risk. While no remote code execution is indicated, the information disclosure and stability impacts can be significant in sensitive environments handling genomic data.

Summary

HTSlib is a widely used C library for reading and writing high-throughput sequencing data formats, including CRAM, a compressed format for DNA sequence alignments. CRAM achieves compression by storing differences relative to an external reference sequence rather than full sequences. During decoding, the reference sequence is loaded into a character array, and the function cram_decode_seq() reconstructs the aligned sequence by copying segments from this reference based on a series of 'features' that describe differences. The vulnerability (CWE-125: Out-of-bounds Read) occurs because cram_decode_seq() does not sufficiently validate the feature data indices, allowing it to read memory before the start or beyond the end of the reference buffer. This out-of-bounds read can cause two main issues: leaking arbitrary memory contents to the caller (potentially exposing sensitive program state information) and causing program crashes due to invalid memory access. The flaw affects htslib versions prior to 1.21.1, versions between 1.22 and 1.22.2, and version 1.23. Fixed versions have been released (1.21.1, 1.22.2, and 1.23.1). The vulnerability can be triggered by processing maliciously crafted CRAM files, requiring no authentication or user interaction, and can be exploited remotely if such files are processed. The CVSS 4.0 score is 6.9, reflecting medium severity with network attack vector, low complexity, and no privileges or user interaction required. No known exploits have been reported in the wild, and no workarounds exist other than upgrading to patched versions.

CWE-125Out-of-bounds Read (opens in a new tab)
Base weaknessCWE Top 25 (2025): #8
The product reads data past the end, or before the beginning, of the intended buffer.
Implementation · Input Validation
Assume all input is malicious. Use an "accept known good" input validation strategy, i.e., use a list of acceptable inputs that strictly conform to specifications. Reject any input that does not strictly conform to specifications, or transform it into something that does.
Architecture and Design · Language Selection
Use a language that provides appropriate memory abstractions.
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
Attack patterns
Overread Buffers (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).
CWE-129Improper Validation of Array Index (opens in a new tab)
Variant weaknessLikelihood of exploit: HighOWASP Top 10 A05:2025: Injection (opens in a new tab)
The product uses untrusted input when calculating or using an array index, but the product does not validate or incorrectly validates the index to ensure the index references a valid position within the array.
Architecture and Design · Input Validation
Use an input validation framework such as Struts or the OWASP ESAPI Validation API. Note that using a framework does not automatically address all input validation problems; be mindful of weaknesses that could arise from misusing the framework itself (CWE-1173).
Architecture and Design
For any security checks that are performed on the client side, ensure that these checks are duplicated on the server side, in order to avoid CWE-602. Attackers can bypass the client-side checks by modifying values after the checks have been performed, or by changing the client to remove the client-side checks…
Requirements · Language Selection
Use a language that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid.
OWASP Cheat Sheets
XML Security (opens in a new tab)
Mass Assignment (opens in a new tab)
Injection Prevention (opens in a new tab)
SQL Injection Prevention (opens in a new tab)
Injection Prevention in Java (opens in a new tab)
OWASP ASVS 4.0.3
V13.3.1 (opens in a new tab)
V5.1.4 (opens in a new tab)
V5.1.3 (opens in a new tab)
Attack patterns
Overflow Buffers (opens in a new tab)
From MITRE CWE, MITRE CAPEC and OWASP (Top 10, OpenCRE).

References

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Exploitation evidence

What to do

Affected software

Description

AI analysisMachine-generated, updated 18 Mar 2026, 19:58 UTC

WeaknessesCWE-125, CWE-129

Technical details

References

Community reviews

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