Evidence used
- No CISA KEV confirmation is currently recorded.
- The selected CVSS metric records a network-reachable, unauthenticated path with no user interaction.
- EPSS is 0.59% for the current model date.
BlackTreeCVE IntelligenceFull vulnerability report · 2026
CVE-2026-31962High confidence
HTSlib CRAM reader has heap buffer overflow due to improper validation of input
samtools · htslib
Official source article: GitHub GHSA-XXMP-V7H3-GPWP ↗. Check the applicable product and release in the original source.
8.8HighCVSS 4.0
Patch only the product branches with a verified fix
Fix availability varies by productHigh technical severity; prioritise exposed affected systems while verifying vendor guidance. Verified remediation exists for at least one product or source, but 4 structured product or package states remain unresolved. Apply remediation only to the exact product branch confirmed by its source.
R
Open reassessment dashboard →Operational reassessment
Published severity in operational context
Published severityHigh→Operational priority:High, unchanged from published severity.unchanged
Compensating controls
- Validate the affected product branch and deploy the verified fixed release.
- Restrict the affected network interface to trusted sources where business-safe.
- Monitor vendor guidance and exploitation sources for a material change.
Verification
- Confirm that the asset runs samtools htslib and falls inside the recorded affected range.
- Verify the installed build against the product-specific fixed version after deployment.
- Validate exposure, authentication requirements and compensating controls in the actual environment.
- Reopen this reassessment when CVSS, KEV, EPSS, exploit evidence or remediation changes.
Remediation availability differs by product scope
Verified remediation exists for at least one product or source, but 4 structured product or package states remain unresolved. Apply remediation only to the exact product branch confirmed by its source.
- Debian Security Tracker: 4 affected package states with no published fix
Distribution package intelligence
5 package statesRelease-specific package status
Debian, ubuntu findings are scoped to the named distribution, release and source package. An absent finding does not mean a package is unaffected.
Package result overrides the generic status
BlackTree has verified remediation for at least one product or source, but the relevant distribution still reports no fixed package for 4 affected package states shown here. Treat those rows as affected with no fix until that distribution publishes a fixed version.
Repository candidate not checked
A published vendor fix does not prove that a matching update is enabled and installable on a particular asset. Confirm the local package candidate before scheduling remediation.
| Distribution release | Source package | Vendor state | Fixed version | Evidence |
|---|---|---|---|---|
| Debian trixietrixie · source | htslib | Affected, no fix publishedDebian currently tracks this release as open. | Not published in this feed | Debian Security Tracker ↗Source updated 5 Oct 2026 |
| Debian bookwormbookworm · source | htslib | Affected, no fix publishedDebian currently tracks this release as open. | Not published in this feed | Debian Security Tracker ↗Source updated 5 Oct 2026 |
| Debian forkyforky · source | htslib | Affected, no fix publishedDebian currently tracks this release as open. | Not published in this feed | Debian Security Tracker ↗Source updated 5 Oct 2026 |
| Debian sidsid · source | htslib | Affected, no fix publishedDebian currently tracks this release as open. | Not published in this feed | Debian Security Tracker ↗Source updated 5 Oct 2026 |
| Ubuntu 24.04 LTSnoble · standard archive | htslib | Under evaluationCanonical reports that the package might be affected and still needs evaluation or fixing. | Not published in this feed | Canonical Ubuntu Security ↗Source updated 5 Oct 2026 |
High technical severity; prioritise exposed affected systems while verifying vendor guidance. Verified remediation exists for at least one product or source, but 4 structured product or package states remain unresolved. Apply remediation only to the exact product branch confirmed by its source.
Fix availability varies by product01
What, why and how
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 `cram_decode_seq()` 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.
What
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 `cram_decode_seq()` 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.
Why
A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc().
How
An attacker operating through a network path may attempt exploitation without authentication or user interaction. If successful, the issue may execute code or commands in the affected security context.
What
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 `cram_decode_seq()` 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.
Why
A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc().
How
An attacker operating through a network path may attempt exploitation without authentication or user interaction. If successful, the issue may execute code or commands in the affected security context.
02
Exploit reality and attack path
CVSS severity, EPSS forecast probability, public exploit material and CISA-confirmed exploitation are separate signals.
Observed exploitation No confirmed evidence
?
Confirmed exploitation and public exploit material are separate signals. Attacks can occur without public proof-of-concept or exploit code.No CISA KEV match was present at the last successful refresh. This means no confirmation from that source, not proof of no exploitation.
Public PoC / exploit material None recorded
?
Confirmed exploitation and public exploit material are separate signals. Attacks can occur without public proof-of-concept or exploit code.No exploit-tagged reference or CISA SSVC proof-of-concept state is currently recorded. Research may still exist outside the structured feeds.
- Likely attack path
- a network path → Heap-based Buffer Overflow → execute code or commands in the affected security context
- Attack surface
- Network
- Privileges required
- None: unauthenticated exploitation is possible
- User interaction
- None
- Attack complexity
- Low: no specialised conditions are recorded
- Security boundary
- Not a CVSS 4.0 base metric
- Weakness
?
CWE means Common Weakness Enumeration: a standard category for the underlying weakness. - CWE-122 ↗
CWE-122: Heap-based Buffer Overflow. A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc().
- CVSS vector
?
CVSS means Common Vulnerability Scoring System. The vector records the metric values used to calculate technical severity. CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:N/VC:L/VI:H/VA:L/SC:N/SI:N/SA:NCommon Vulnerability Scoring System 4.0: the compact vector below is decoded into plain language.
AVNetworkAttack vector: The vulnerable component can be reached over a network.ACLowAttack complexity: No specialised conditions are required beyond attacker-controlled input.ATNoneAttack requirements: No additional deployment or execution condition is required.PRNonePrivileges required: The attacker does not need an account or existing privileges.UINoneUser interaction: No action by another user is required.VCLowVulnerable-system confidentiality: A successful attack can cause a limited loss.VIHighVulnerable-system integrity: A successful attack can cause a major loss.VALowVulnerable-system availability: A successful attack can cause a limited loss.SCNoneSubsequent-system confidentiality: No direct loss is represented by this metric.SINoneSubsequent-system integrity: No direct loss is represented by this metric.SANoneSubsequent-system availability: No direct loss is represented by this metric.- Post-exploitation / living off the land
- After compromise, an attacker may use built-in shells, scripting engines, scheduled tasks and native network utilities for discovery, persistence or movement. This is a plausible LoTL path, not evidence that it has occurred for every attack.
03
Patch and workaround
Operational remediation based on structured source evidence.
- Status
?
Patch availability is based on structured fixed-version fields and authoritative update references. If no fix is verified, check the vendor advisory before making a change. - Fix availability varies by product
- Action
- Use the product-specific evidence above. Patch only products with a verified fixed release, and keep every affected or under-investigation state without a matching fix in the remediation queue.
- Workaround
- No verified workaround is recorded. If business-safe, reduce exposure to the affected interface and allow only trusted sources until authoritative guidance is available.
04
Evidence and provenance
Published 18 Mar 2026 · Last source change 18 Mar 2026, 18:37 UTC · CWE-122 · Heap-based Buffer Overflow
CVE recordCVE.org · 5.2
CVSS sourceCNA
EPSS source FIRST · tracked since 2026-08-14
?
The date BlackTree first stored a score for this CVE from the daily FIRST EPSS feed.European sourceENISA EUVD · EUVD-2026-12923
Product sourceCNA
Remediation sourceCVE/CNA references
CWE sourceCNA
NVD statusNVD enriched
Core structured fields are present and their contributing authorities are shown above.
Material change intelligence
View recent updates ↗What changed after publication
No material field changes have been recorded since change tracking began. Routine source refreshes and cosmetic edits are intentionally excluded.
CVE published
Fixed release or patch reference recorded
Technical terms and abbreviations used in this report
- CVE
- Common Vulnerabilities and Exposures: the public identifier for one disclosed vulnerability.
- CVSS
- Common Vulnerability Scoring System: a technical severity framework; it is not patching priority by itself.
- EPSS
- Exploit Prediction Scoring System: FIRST's estimate of the probability that exploitation activity will be observed in the next 30 days; it is a forecast, not confirmation.
- CWE
- Common Weakness Enumeration: the standard category describing the underlying software or hardware weakness.
- CNA
- CVE Numbering Authority: an organisation authorised to assign and publish CVE records.
- CISA ADP
- Cybersecurity and Infrastructure Security Agency Authorized Data Publisher: structured enrichment added to a CVE record.
- NVD
- National Vulnerability Database: NIST's enrichment service for CVE records.
- CERT / CSIRT
- A computer security incident response team that publishes warnings or coordinates incident response.
- PoC
- Proof of concept: public material that demonstrates or helps reproduce exploitation.
- CSAF
- Common Security Advisory Framework: a machine-readable format for security advisories.
- LoTL
- Living off the land: abuse of legitimate tools or system functions during an attack.